gromacs →
2019.3-2 →
armhf → 2019-08-23 22:01:20
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on test2019
+==============================================================================+
| gromacs 2019.3-2 (armhf) Fri, 23 Aug 2019 14:46:13 +0000 |
+==============================================================================+
Package: gromacs
Version: 2019.3-2
Source Version: 2019.3-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-3ca42f73-dd26-4564-aff5-9c763c8212d3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.5 MB in 25s (996 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 33.5 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2019.3-2 (dsc) [2578 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2019.3-2 (tar) [33.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2019.3-2 (diff) [36.1 kB]
Fetched 33.5 MB in 11s (3155 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-xnRizR/gromacs-2019.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-xnRizR' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-OC1cwH/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-OC1cwH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-OC1cwH/gpg/trustdb.gpg: trustdb created
gpg: key E70254B6505CF8F7: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key E70254B6505CF8F7: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key E70254B6505CF8F7: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3216 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-OC1cwH/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 88 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12044 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper (>= 12), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-OC1cwH/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Sources [572 B]
Get:5 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Packages [655 B]
Fetched 2560 B in 1s (3815 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-OC1cwH/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath cmake
cmake-data cpp-8 debhelper dh-autoreconf dh-strip-nondeterminism dwz file
g++-8 gcc-8 gcc-8-base gcc-9-base gettext gettext-base gfortran gfortran-8
groff-base hwloc-nox ibverbs-providers intltool-debian libarchive-zip-perl
libarchive13 libasan5 libatomic1 libblas-dev libblas3 libboost-dev
libboost1.67-dev libbsd0 libcc1-0 libcroco3 libcurl4 libedit2 libelf1
libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libexpat1
libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-single3
libfile-stripnondeterminism-perl libgcc-8-dev libgcc1 libgfortran-8-dev
libgfortran5 libglib2.0-0 libgomp1 libgssapi-krb5-2 libhwloc-dev
libhwloc-plugins libhwloc5 libibverbs-dev libibverbs1 libicu63 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmpich-dev libmpich12
libncurses6 libncursesw6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libopenmpi-dev libopenmpi3 libpciaccess0
libpipeline1 libpmix2 libprocps7 libpsl5 libpthread-stubs0-dev librhash0
librtmp1 libsigsegv2 libssh2-1 libssl1.1 libstdc++-8-dev libstdc++6
libsub-override-perl libtinfo5 libtinfo6 libtool libubsan1 libuchardet0
libuv1 libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1
libxcb1-dev libxdmcp-dev libxdmcp6 libxml2 m4 man-db mpich
ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf
procps sensible-utils x11proto-core-dev x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build gcc-8-locales dh-make gcc-8-doc
libstdc++6-8-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan5-dbg liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg
libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-8-doc libgfortran5-dbg libcoarrays-dev groff lrzip liblapack-doc
libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libfftw3-doc krb5-doc krb5-user libhwloc-contrib-plugins libtool-doc
openmpi-doc pciutils libstdc++-8-doc gcj-jdk libx11-doc libxcb-doc m4-doc
apparmor less www-browser mpich-doc opencl-icd keychain libpam-ssh
monkeysphere ssh-askpass libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 libcoarrays-openmpi-dev
publicsuffix xauth libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils chrpath cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file
gcc-9-base gettext gettext-base gfortran gfortran-8 groff-base hwloc-nox
ibverbs-providers intltool-debian libarchive-zip-perl libarchive13
libblas-dev libblas3 libboost-dev libboost1.67-dev libbsd0 libcroco3
libcurl4 libedit2 libelf1 libevent-2.1-6 libevent-core-2.1-6
libevent-pthreads-2.1-6 libexpat1 libfftw3-bin libfftw3-dev libfftw3-double3
libfftw3-single3 libfile-stripnondeterminism-perl libgfortran-8-dev
libgfortran5 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins
libhwloc5 libibverbs-dev libibverbs1 libicu63 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libltdl-dev
libltdl7 libmagic-mgc libmagic1 libmpich-dev libmpich12 libncurses6
libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev
libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix2 libprocps7
libpsl5 libpthread-stubs0-dev librhash0 librtmp1 libsigsegv2 libssh2-1
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libuv1
libx11-6 libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev
libxdmcp-dev libxdmcp6 libxml2 m4 man-db mpich ocl-icd-libopencl1
openmpi-bin openmpi-common openssh-client po-debconf procps
sbuild-build-depends-gromacs-dummy sensible-utils x11proto-core-dev
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libncursesw6 libstdc++-8-dev libstdc++6 libtinfo6 libubsan1
15 upgraded, 115 newly installed, 0 to remove and 73 not upgraded.
Need to get 83.3 MB of archives.
After this operation, 310 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-OC1cwH/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.1.0-10+rpi1 [190 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libgcc1 armhf 1:9.1.0-10+rpi1 [37.0 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 9.1.0-10+rpi1 [413 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.6.1-1 [1248 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20190803-1 [318 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20190803-1 [104 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 9.1.0-10+rpi1 [112 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf g++-8 armhf 8.3.0-19+rpi1 [7184 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf gcc-8 armhf 8.3.0-19+rpi1 [6893 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf cpp-8 armhf 8.3.0-19+rpi1 [6487 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 9.1.0-10+rpi1 [38.0 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 9.1.0-10+rpi1 [73.8 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 9.1.0-10+rpi1 [8164 B]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libasan5 armhf 9.1.0-10+rpi1 [347 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-8-dev armhf 8.3.0-19+rpi1 [1551 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libgcc-8-dev armhf 8.3.0-19+rpi1 [595 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf gcc-8-base armhf 8.3.0-19+rpi1 [192 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-5 [253 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-5 [111 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-5 [66.2 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20190324-1 [78.9 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.0p1-4 [692 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.13.4-1 [1476 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.3.3-4 [270 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.65.3-1 [300 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.7-1 [77.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.8-1 [132 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.30.1-1 [102 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.13.4-1 [2559 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.5.0-1 [22.8 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.5.0-1 [14.1 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.60.6-2 [1109 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.5.3 [1036 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.1.0-10+rpi1 [230 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-8-dev armhf 8.3.0-19+rpi1 [249 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf gfortran-8 armhf 8.3.0-19+rpi1 [6855 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:8.3.0-1+rpi2 [1428 B]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-9 [387 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libhwloc5 armhf 1.11.13-1+rpi1 [87.4 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 1.11.13-1+rpi1 [144 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 24.0-2 [44.1 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 24.0-2 [20.5 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.8.0-2 [113 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2 [4184 B]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-9 [159 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 1.11.13-1+rpi1 [143 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.12-2 [35.7 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 1.11.13-1+rpi1 [16.1 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 24.0-2 [187 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.8.0-2 [1551 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.3-3 [1028 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.3-3 [332 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.3-3 [1198 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 3.1.4-1 [433 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 3.1.3-11+rpi1 [1813 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 3.1.3-11+rpi1 [164 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 3.1.3-11+rpi1 [197 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 3.1.3-11+rpi1 [964 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2018.4-4 [251 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2018.4-4 [3128 B]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.13.1-2 [169 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.7-1 [760 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:armhf (2.2.7-1) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libpciaccess0:armhf (0.14-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
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Setting up libglib2.0-0:armhf (2.60.6-2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1c-1) ...
Setting up libprocps7:armhf (2:3.3.15-2) ...
Setting up libnghttp2-14:armhf (1.39.2-1) ...
Setting up libmagic1:armhf (1:5.37-5) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.37-5) ...
Setting up libgomp1:armhf (9.1.0-10+rpi1) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up libasan5:armhf (9.1.0-10+rpi1) ...
Setting up xtrans-dev (1.3.5-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libuv1:armhf (1.30.1-1) ...
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up libncurses6:armhf (6.1+20190803-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libatomic1:armhf (9.1.0-10+rpi1) ...
Setting up gcc-8-base:armhf (8.3.0-19+rpi1) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libltdl7:armhf (2.4.6-9) ...
Setting up libfftw3-double3:armhf (3.3.8-2) ...
Setting up libevent-core-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libgfortran5:armhf (9.1.0-10+rpi1) ...
Setting up libevent-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libubsan1:armhf (9.1.0-10+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libmpich12:armhf (3.3-3) ...
Setting up sensible-utils (0.0.12) ...
Setting up ocl-icd-libopencl1:armhf (2.2.12-2) ...
Setting up librhash0:armhf (1.3.8-1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up procps (2:3.3.15-2) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up openmpi-common (3.1.3-11+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up xorg-sgml-doctools (1:1.11-1) ...
Setting up cmake-data (3.13.4-1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
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Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20190803-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up libcc1-0:armhf (9.1.0-10+rpi1) ...
Setting up chrpath (0.16-2) ...
Setting up libjsoncpp1:armhf (1.7.4-3) ...
Setting up x11proto-dev (2018.4-4) ...
Setting up libfile-stripnondeterminism-perl (1.5.0-1) ...
Setting up libevent-pthreads-2.1-6:armhf (2.1.8-stable-4) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
Setting up libxau-dev:armhf (1:1.0.8-1+b2) ...
Setting up libtool (2.4.6-9) ...
Setting up libarchive13:armhf (3.3.3-4) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up libhwloc5:armhf (1.11.13-1+rpi1) ...
Setting up libedit2:armhf (3.1-20190324-1) ...
Setting up hwloc-nox (1.11.13-1+rpi1) ...
Setting up m4 (1.4.18-2) ...
Setting up libhwloc-plugins:armhf (1.11.13-1+rpi1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libblas3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up x11proto-core-dev (2018.4-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up libgcc-8-dev:armhf (8.3.0-19+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up libcurl4:armhf (7.65.3-1) ...
Setting up libx11-6:armhf (2:1.6.7-1) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up libblas-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libstdc++-8-dev:armhf (8.3.0-19+rpi1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libgfortran-8-dev:armhf (8.3.0-19+rpi1) ...
Setting up libibverbs1:armhf (24.0-2) ...
Setting up liblapack3:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.19.8.1-9) ...
Setting up gcc-8 (8.3.0-19+rpi1) ...
Setting up libxcb1-dev:armhf (1.13.1-2) ...
Setting up libpmix2:armhf (3.1.4-1) ...
Setting up ibverbs-providers:armhf (24.0-2) ...
Setting up mpich (3.3-3) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
Setting up openssh-client (1:8.0p1-4) ...
Setting up gfortran-8 (8.3.0-19+rpi1) ...
Setting up libopenmpi3:armhf (3.1.3-11+rpi1) ...
Setting up libx11-dev:armhf (2:1.6.7-1) ...
Setting up man-db (2.8.6.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:8.3.0-1+rpi2) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-9) ...
Setting up liblapack-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libmpich-dev:armhf (3.3-3) ...
update-alternatives: using /usr/include/arm-linux-gnueabihf/mpich to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up g++-8 (8.3.0-19+rpi1) ...
Setting up cmake (3.13.4-1) ...
Setting up libhwloc-dev:armhf (1.11.13-1+rpi1) ...
Setting up libboost-dev:armhf (1.67.0.2) ...
Setting up openmpi-bin (3.1.3-11+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up po-debconf (1.0.21) ...
Setting up libibverbs-dev:armhf (24.0-2) ...
Setting up libopenmpi-dev:armhf (3.1.3-11+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.5.3) ...
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.5.0-1) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ armhf (armv7l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-19+rpi1 gcc-8_8.3.0-19+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-19+rpi1 libstdc++6_9.1.0-10+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 chrpath_0.16-2 cmake_3.13.4-1 cmake-data_3.13.4-1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-19+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.5.3 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.5.0-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.37-5 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-19+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-19+rpi1 gcc-8-base_8.3.0-19+rpi1 gcc-9-base_9.1.0-10+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:8.3.0-1+rpi2 gfortran-8_8.3.0-19+rpi1 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 hwloc-nox_1.11.13-1+rpi1 ibverbs-providers_24.0-2 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-4 libasan5_9.1.0-10+rpi1 libassuan0_2.5.2-1 libatomic1_9.1.0-10+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.2 libboost1.67-dev_1.67.0-13 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_9.1.0-10+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.13-1 libcurl4_7.65.3-1 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libedit2_3.1-20190324-1 libelf1_0.176-1.1 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.7-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfile-stripnondeterminism-perl_1.5.0-1 libgcc-8-dev_8.3.0-19+rpi1 libgcc1_1:9.1.0-10+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgfortran-8-dev_8.3.0-19+rpi1 libgfortran5_9.1.0-10+rpi1 libglib2.0-0_2.60.6-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_9.1.0-10+rpi1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-6+b1 libhogweed4_3.4.1-1 libhwloc-dev_1.11.13-1+rpi1 libhwloc-plugins_1.11.13-1+rpi1 libhwloc5_1.11.13-1+rpi1 libibverbs-dev_24.0-2 libibverbs1_24.0-2 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 libltdl-dev_2.4.6-9 libltdl7_2.4.6-9 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpich-dev_3.3-3 libmpich12_3.3-3 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnghttp2-14_1.39.2-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-1 libopenmpi-dev_3.1.3-11+rpi1 libopenmpi3_3.1.3-11+rpi1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpciaccess0_0.14-1 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpmix2_3.1.4-1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpthread-stubs0-dev_0.4-1 libreadline7_7.0-5 librhash0_1.3.8-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-19+rpi1 libstdc++6_9.1.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-9 libubsan1_9.1.0-10+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libuv1_1.30.1-1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libx11-dev_2:1.6.7-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb1_1.13.1-2 libxcb1-dev_1.13.1-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.6.1-1 mawk_1.3.3-17 mount_2.33.1-0.1 mpich_3.3-3 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 ocl-icd-libopencl1_2.2.12-2 openmpi-bin_3.1.3-11+rpi1 openmpi-common_3.1.3-11+rpi1 openssh-client_1:8.0p1-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Jul 13 03:33:10 2019 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2019.3-2.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2019.3.orig.tar.gz
dpkg-source: info: unpacking gromacs_2019.3-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying doxygen.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/buildd
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=116
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-3ca42f73-dd26-4564-aff5-9c763c8212d3
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_ID=c39103
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2019.3-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON)
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- hwloc version: 1.11.13
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.13", minimum required is "1.5")
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found X11: /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Can not build documentation with Python 3
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:229 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- hwloc version: 1.11.13
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.13", minimum required is "1.5")
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Found X11: /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Can not build documentation with Python 3
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 1.11.13
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.13", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/mpicc.mpich
-- Check for working C compiler: /usr/bin/mpicc.mpich -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:229 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 1.11.13
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.13", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 1.11.13
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.13", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /usr/bin/mpicc.openmpi
-- Check for working C compiler: /usr/bin/mpicc.openmpi -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Performing Test CXXFLAG_STD_CXX0X
-- Performing Test CXXFLAG_STD_CXX0X - Success
-- Performing Test CXX11_SUPPORTED
-- Performing Test CXX11_SUPPORTED - Success
-- Performing Test CXX11_STDLIB_PRESENT
-- Performing Test CXX11_STDLIB_PRESENT - Success
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:229 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- hwloc version: 1.11.13
-- Found Hwloc: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "1.11.13", minimum required is "1.5")
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 3 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 0
-- Detected build CPU stepping - 3
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Looking for C++ include regex
-- Looking for C++ include regex - found
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_MISSING_DECL
-- Performing Test HAS_NO_MISSING_DECL - Success
-- Performing Test HAS_NO_MISSING_PROTO
-- Performing Test HAS_NO_MISSING_PROTO - Failed
-- Performing Test HAS_NO_MSVC_UNUSED
-- Performing Test HAS_NO_MSVC_UNUSED - Failed
-- Performing Test HAS_DECL_IN_SOURCE
-- Performing Test HAS_DECL_IN_SOURCE - Failed
-- Check if the system is big endian
-- Searching 16 bit integer
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
"%4d-%02d-%02d %02d:%02d:%02d",
^~~~
In file included from /usr/include/stdio.h:873,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 5%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 7%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 9%] Built target mdrun_test_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3243833 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
^
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
vectorSecondDerivative(ArrayRef<const double> f, double spacing)
^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/variant.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
}
^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
updateForceCorrelationGrid(probWeightNeighbor, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tempForce_, biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceFromNeighbor);
~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleProbabilityWeights(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleCoordAndPmf(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
CoordState::sampleUmbrellaGridpoint(const Grid &grid,
^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void CorrelationTensor::addData(double weight,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSize(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.4 -o ../../lib/libgromacs.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -fopenmp -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.4.0.0 ../../lib/libgromacs.so.4 ../../lib/libgromacs.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/share/template /<<PKGBUILDDIR>>/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
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/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:371:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
atomsArrayRef);
~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:371:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
"%4d-%02d-%02d %02d:%02d:%02d",
^~~~
In file included from /usr/include/stdio.h:873,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 5%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 7%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target mdrun_test_objlib
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3243833 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
static void low_set_ddbox(int numPbcDimensions,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void set_ddbox(const gmx_domdec_t &dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions,
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&dd.nc, box, calculateUnboundedSize, xRef,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddbox);
~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void set_ddbox_cr(const t_commrec &cr,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir),
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dd_nc, box, true, x, nullptr, ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void dd_collect_vec(gmx_domdec_t *dd,
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(const gmx_domdec_t *dd,
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, false, state.box, true, state.x, &ddbox);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog,
^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::LocalAtomSetManager*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog,
^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions,
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mtop, ir,
~~~~~~~~~
box, xGlobal,
~~~~~~~~~~~~~
&ddbox);
~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirForward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void dd_move_x(gmx_domdec_t *dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void dd_move_f(gmx_domdec_t *dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv(dd, d, dddirForward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
work.positionBuffer, rvecBufferRef);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
rvec *makeRvecArray(gmx::ArrayRef<const gmx::RVec> v,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, true,
~~~~~~~~~^~~~~~~~~~~
DDMASTER(dd) ? state_global->box : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
true, xGlobal,
~~~~~~~~~~~~~~
&ddbox);
~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, bMasterState, state_local->box,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
true, state_local->x, &ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, bMasterState, state_local->box,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bNStGlobalComm, state_local->x, &ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_local->x);
~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_local->x);
~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0,
~~
comm->zones.size[0].bb_x0,
~~~~~~~~~~~~~~~~~~~~~~~~~~
comm->zones.size[0].bb_x1,
~~~~~~~~~~~~~~~~~~~~~~~~~~
comm->updateGroupsCog.get(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, dd->ncg_home,
~~~~~~~~~~~~~~~~
comm->zones.dens_zone0,
~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo,
~~~~~~~~~~~
state_local->x,
~~~~~~~~~~~~~~~
ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->nbv->grp[eintLocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->nbv->nbat);
~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
vectorSecondDerivative(ArrayRef<const double> f, double spacing)
^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/variant.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/__/external/vmd_molfile/vmddlopen.c.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:51:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx_bool, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
bool pullCheckPbcWithinGroup(const pull_t &pull,
^~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
}
^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2255:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
updateForceCorrelationGrid(probWeightNeighbor, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tempForce_, biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:463:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceFromNeighbor);
~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:487:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleProbabilityWeights(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleCoordAndPmf(const Grid &grid,
^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
CoordState::sampleUmbrellaGridpoint(const Grid &grid,
^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void CorrelationTensor::addData(double weight,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSize(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_anadock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anadock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tune_pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:1702:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
positionsArrayRef);
~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:1702:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:373:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:373:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:316:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjconv.cpp:316:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval,
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:67:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:99:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:174:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:206:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval,
^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp-impl.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp-impl.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'int enter_params(gmx_ffparams_t*, t_functype, real*, int, real, int, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert-molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert-molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, gmx_atomprop_t, real, real)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:537:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
pullCheckPbcWithinGroup(*pull_work,
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(x),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mtop->natoms),
~~~~~~~~~~~~~~
pbc, g, c_pullGroupSmallGroupThreshold);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:564:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
pullCheckPbcWithinGroup(*pull_work,
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(x),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mtop->natoms),
~~~~~~~~~~~~~~
pbc, g, c_pullGroupPbcMargin);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
/usr/include/c++/8/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >'} changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:610:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
AnalysisDataStorageFrameData::addPointSet(int dataSetIndex, int firstColumn,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:750:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
data_->addPointSet(currentDataSet_, firstColumn,
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
makeConstArrayRef(values_).
~~~~~~~~~~~~~~~~~~~~~~~~~~~
subArray(begin, end-begin));
~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:750:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/tools/report-methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report-methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/chargegroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation-utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
BoxDeformation::apply(ArrayRef<RVec> x,
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void calc_mu(int start, int homenr, gmx::ArrayRef<gmx::RVec> x, const real q[], const real qB[],
^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
static void constr_recur(const t_blocka *at2con,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
t_blocka make_at2con(const gmx_moltype_t &moltype,
^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const gmx_bool*, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void andersen_tcoupl(const t_inputrec *ir, int64_t step,
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda *fepvals)
^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdsetup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(f_global), f_local.size()));
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void nbnxn_put_on_grid(nbnxn_search_t nbs,
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
zone, c0, c1,
~~~~~~~~~~~~~
nullptr,
~~~~~~~~
zones->cg_range[zone],
~~~~~~~~~~~~~~~~~~~~~~
zones->cg_range[zone+1],
~~~~~~~~~~~~~~~~~~~~~~~~
-1,
~~~
atinfo,
~~~~~~~
x,
~~
0, nullptr,
~~~~~~~~~~~
nb_kernel_type,
~~~~~~~~~~~~~~~
nbat);
~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
int add_binr(t_bin *b, gmx::ArrayRef<const real> r)
^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void extract_binr(t_bin *b, int index, gmx::ArrayRef<real> r)
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdstep, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceWithPadding[Min], force_vir, md, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1, nrnb, wcycle,
~~~~~~~~~~~~~~~~
top, groups, state->box, posWithPadding[Try], &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceWithPadding[Try], force_vir,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
md, enerd, fcd, state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shellfc_flags,
~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(FILE *fplog,
^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2721:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2119:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void do_force(FILE *fplog,
^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, vzero, box_diag,
~~~~~~~~~~~~~~~~~~~
nullptr, 0, mdatoms->homenr, -1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo, x.unpaddedArrayRef(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, nullptr,
~~~~~~~~~~~
nbv->grp[eintLocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->nbat);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd),
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo, x.unpaddedArrayRef(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->grp[eintNonlocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->nbat);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, wcycle,
~~~~~~~~~~~~~~~~
fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flags, &forceWithVirial, enerd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ed, bNS);
~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1626:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2047:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, wcycle,
~~~~~~~~~~~~~~~~
fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flags, &forceWithVirial, enerd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ed, bNS);
~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2058:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2069:26: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2874:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0)
^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(FILE *fplog,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, state, state_global, observablesHistory, f);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
upd->deform->apply(localX, state->box, step);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_update_t*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
andersen_tcoupl(ir, step, cr, md, v, rate,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
upd->sd->randomize_group, upd->sd->boltzfac);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
^~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
/usr/include/c++/8/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wnblist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/disre.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void constructVsitesGlobal(const gmx_mtop_t &mtop,
^~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/gpubonded-impl.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-internal.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.3':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/manage-threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/position-restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate-spline-moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald-utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long-range-correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-load-balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-pp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-redistribute.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-solve.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spline-work.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program-impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/integrator.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/logging.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
count, nrnb, wcycle, top, &top_global->groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_NS : 0),
~~~~~~~~~~~~~~~~~~~~~~~~~
DOMAINDECOMP(cr) ?
~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::yes :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::no,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DOMAINDECOMP(cr) ?
~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::yes :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::no);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:875:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_NS : 0) | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1026:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1051:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
checkpointHandler->isCheckpointingStep(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bRerunMD, bLastStep,
~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1089:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1292:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NS | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
isCheckpointingStep, doRerun, isLastStep,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<real>(step), &ems.s, state_global, observablesHistory, ems.f);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NS | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
isCheckpointingStep, doRerun, isLastStep,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state, flocal, ftemp);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mimicCommunicator.sendForces(ftemp, state_global->natoms);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, &top_global->groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_global->lambda,
~~~~~~~~~~~~~~~~~~~~~
nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bStateChanged ? GMX_FORCE_STATECHANGED : 0),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::no,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::no);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:922:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&mtop, inputrec,
~~~~~~~~~~~~~~~~
box, positionsFromStatePointer(globalState.get()),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&atomSets);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1278:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
constructVsitesGlobal(mtop, globalState->x);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/mdmodules.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
^~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs_d.so.4 -o ../../lib/libgromacs_d.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -fopenmp -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.4.0.0 ../../lib/libgromacs_d.so.4 ../../lib/libgromacs_d.so
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/share/template /<<PKGBUILDDIR>>/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
Scanning dependencies of target template
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cd /<<PKGBUILDDIR>>/build/basic-dp/share/template && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.4.0.0 -fopenmp /usr/lib/arm-linux-gnueabihf/libX11.so -lm
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cd /<<PKGBUILDDIR>>/build/basic-dp/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs_d.so.4.0.0 -fopenmp -lm
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest /<<PKGBUILDDIR>>/build/basic/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
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[ 0%] Built target lmfit_objlib
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[ 2%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
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Scanning dependencies of target gmock
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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[ 3%] Built target mdrun_objlib
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
[ 6%] Built target libgromacs_external
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
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[ 19%] Built target libgromacs_generated
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
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[ 19%] Built target onlinehelp-test-shared
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target listed-forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
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/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 83%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target ewald-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
[ 84%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target mdrunutility-mpi-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/bits/random.h:34,
from /usr/include/c++/8/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target fileio-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target pull-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target pdb2gmx-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target simd-test
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
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[ 94%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
Scanning dependencies of target selection-test
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
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cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
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cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report-methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target tool-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target legacy-mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target trajectoryanalysis-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target legacy-mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target mdrun-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (3 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (19 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariants
1: [ OK ] ReferenceDataTest.HandlesVariants (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms)
1: [----------] 34 tests from ReferenceDataTest (47 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (9 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (77 ms total)
1: [ PASSED ] 59 tests.
1/40 Test #1: TestUtilsUnitTests ............... Passed 0.33 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (10 ms)
2: [----------] 1 test from MpiSelfTest (11 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (11 ms total)
2: [ PASSED ] 1 test.
2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.05 sec
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3: [==========] Running 50 tests from 8 test cases.
3: [----------] Global test environment set-up.
3: [----------] 1 test from VerletBufferConstraintTest
3: [ RUN ] VerletBufferConstraintTest.EqualMasses
3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
3: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
3:
3: [----------] 3 tests from PrintEbin
3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (2 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (2 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (1 ms)
3: [----------] 3 tests from PrintEbin (6 ms total)
3:
3: [----------] 4 tests from ShakeTest
3: [ RUN ] ShakeTest.ConstrainsOneBond
3: [ OK ] ShakeTest.ConstrainsOneBond (1 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
3: [----------] 4 tests from ShakeTest (1 ms total)
3:
3: [----------] 1 test from NullSignalTest
3: [ RUN ] NullSignalTest.NullSignallerWorks
3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
3: [----------] 1 test from NullSignalTest (0 ms total)
3:
3: [----------] 7 tests from SignalTest
3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
3: [----------] 7 tests from SignalTest (0 ms total)
3:
3: [----------] 9 tests from UpdateGroups
3: [ RUN ] UpdateGroups.ethaneUA
3: [ OK ] UpdateGroups.ethaneUA (1 ms)
3: [ RUN ] UpdateGroups.methane
3: [ OK ] UpdateGroups.methane (0 ms)
3: [ RUN ] UpdateGroups.ethane
3: [ OK ] UpdateGroups.ethane (0 ms)
3: [ RUN ] UpdateGroups.butaneUA
3: [ OK ] UpdateGroups.butaneUA (0 ms)
3: [ RUN ] UpdateGroups.waterThreeSite
3: [ OK ] UpdateGroups.waterThreeSite (1 ms)
3: [ RUN ] UpdateGroups.waterFourSite
3: [ OK ] UpdateGroups.waterFourSite (0 ms)
3: [ RUN ] UpdateGroups.fourAtomsWithSettle
3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
3: [ RUN ] UpdateGroups.waterFlexAngle
3: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
3: [ RUN ] UpdateGroups.twoMoltypes
3: [ OK ] UpdateGroups.twoMoltypes (0 ms)
3: [----------] 9 tests from UpdateGroups (2 ms total)
3:
3: [----------] 1 test from UpdateGroupsCog
3: [ RUN ] UpdateGroupsCog.ComputesCogs
3: [ OK ] UpdateGroupsCog.ComputesCogs (17 ms)
3: [----------] 1 test from UpdateGroupsCog (18 ms total)
3:
3: [----------] 24 tests from WithParameters/SettleTest
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms)
3: [----------] 24 tests from WithParameters/SettleTest (4 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 50 tests from 8 test cases ran. (33 ms total)
3: [ PASSED ] 50 tests.
3/40 Test #3: MdlibUnitTest .................... Passed 0.10 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4: [==========] Running 3 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 3 tests from ElectricFieldTest
4: [ RUN ] ElectricFieldTest.Static
4: [ OK ] ElectricFieldTest.Static (2 ms)
4: [ RUN ] ElectricFieldTest.Oscillating
4: [ OK ] ElectricFieldTest.Oscillating (0 ms)
4: [ RUN ] ElectricFieldTest.Pulsed
4: [ OK ] ElectricFieldTest.Pulsed (1 ms)
4: [----------] 3 tests from ElectricFieldTest (3 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 3 tests from 1 test case ran. (3 ms total)
4: [ PASSED ] 3 tests.
4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.06 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 15 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 15 tests from BondedTest
5: [ RUN ] BondedTest.BondAnglePbcNone
5: [ OK ] BondedTest.BondAnglePbcNone (1 ms)
5: [ RUN ] BondedTest.BondAnglePbcXy
5: [ OK ] BondedTest.BondAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.BondAnglePbcXyz
5: [ OK ] BondedTest.BondAnglePbcXyz (1 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcNone
5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXy
5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXyz
5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcNo
5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXy
5: [ OK ] BondedTest.IfuncBondsPbcXy (1 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXyz
5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcNo
5: [ OK ] BondedTest.IfuncAnglesPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXy
5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ
5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo
5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms)
5: [----------] 15 tests from BondedTest (6 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 15 tests from 1 test case ran. (8 ms total)
5: [ PASSED ] 15 tests.
5/40 Test #5: ListedForcesTest ................. Passed 0.06 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6: [==========] Running 55 tests from 6 test cases.
6: [----------] Global test environment set-up.
6: [----------] 3 tests from CommandLineHelpModuleTest
6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (3 ms)
6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (19 ms)
6: [----------] 3 tests from CommandLineHelpModuleTest (23 ms total)
6:
6: [----------] 6 tests from CommandLineHelpWriterTest
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
6: [----------] 6 tests from CommandLineHelpWriterTest (7 ms total)
6:
6: [----------] 6 tests from CommandLineModuleManagerTest
6: [ RUN ] CommandLineModuleManagerTest.RunsModule
6: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
6: [----------] 6 tests from CommandLineModuleManagerTest (4 ms total)
6:
6: [----------] 13 tests from CommandLineParserTest
6: [ RUN ] CommandLineParserTest.HandlesSingleValues
6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesString
6: [ OK ] CommandLineParserTest.HandlesString (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (1 ms)
6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
6: [----------] 13 tests from CommandLineParserTest (3 ms total)
6:
6: [----------] 6 tests from CommandLineProgramContextTest
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
6:
6: [----------] 21 tests from ParseCommonArgsTest
6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (1 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (1 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (3 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (5 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (1 ms)
6: [----------] 21 tests from ParseCommonArgsTest (18 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 55 tests from 6 test cases ran. (58 ms total)
6: [ PASSED ] 55 tests.
6/40 Test #6: CommandLineUnitTests ............. Passed 0.11 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 9 tests from 2 test cases.
7: [----------] Global test environment set-up.
7: [----------] 7 tests from HashedMap
7: [ RUN ] HashedMap.InsertsFinds
7: [ OK ] HashedMap.InsertsFinds (0 ms)
7: [ RUN ] HashedMap.NegativeKeysWork
7: [ OK ] HashedMap.NegativeKeysWork (0 ms)
7: [ RUN ] HashedMap.InsertsErases
7: [ OK ] HashedMap.InsertsErases (0 ms)
7: [ RUN ] HashedMap.InsertsOrAssigns
7: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
7: [ RUN ] HashedMap.Clears
7: [ OK ] HashedMap.Clears (0 ms)
7: [ RUN ] HashedMap.LinkedEntries
7: [ OK ] HashedMap.LinkedEntries (0 ms)
7: [ RUN ] HashedMap.ResizesTable
7: [ OK ] HashedMap.ResizesTable (0 ms)
7: [----------] 7 tests from HashedMap (0 ms total)
7:
7: [----------] 2 tests from LocalAtomSetManager
7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
7: [----------] 2 tests from LocalAtomSetManager (1 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 9 tests from 2 test cases ran. (2 ms total)
7: [ PASSED ] 9 tests.
7/40 Test #7: DomDecTests ...................... Passed 0.06 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 257 tests from 10 test cases.
8: [----------] Global test environment set-up.
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (1 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (13 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (16 ms total)
8:
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (22 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (14 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (33 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (15 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (15 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (15 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (15 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (15 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (17 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (17 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (17 ms)
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (392 ms total)
8:
8: [----------] 144 tests from SaneInput/PmeGatherTest
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (7 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (7 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (4 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (7 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
8: [----------] 144 tests from SaneInput/PmeGatherTest (236 ms total)
8:
8: [----------] 16 tests from SaneInput/PmeSolveTest
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (6 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (6 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (7 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (5 ms)
8: [----------] 16 tests from SaneInput/PmeSolveTest (70 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (31 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (54 ms total)
8:
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (8 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (6 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (6 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (2 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (3 ms)
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (64 ms total)
8:
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (10 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (7 ms)
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (72 ms total)
8:
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (8 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (10 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (35 ms)
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (110 ms total)
8:
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (16 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (16 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (22 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (25 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (32 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (35 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (14 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (14 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (18 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (24 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (24 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (28 ms)
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (286 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 257 tests from 10 test cases ran. (1482 ms total)
8: [ PASSED ] 257 tests.
8/40 Test #8: EwaldUnitTests ................... Passed 1.68 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 14 tests from 4 test cases.
9: [----------] Global test environment set-up.
9: [----------] 2 tests from ManyFFTTest
9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (50 ms)
9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (57 ms)
9: [----------] 2 tests from ManyFFTTest (111 ms total)
9:
9: [----------] 1 test from FFTTest
9: [ RUN ] FFTTest.Real2DLength18_15Test
9: [ OK ] FFTTest.Real2DLength18_15Test (21 ms)
9: [----------] 1 test from FFTTest (22 ms total)
9:
9: [----------] 1 test from FFFTest3D
9: [ RUN ] FFFTest3D.Real5_6_9
9: [ OK ] FFFTest3D.Real5_6_9 (15 ms)
9: [----------] 1 test from FFFTest3D (17 ms total)
9:
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (3 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (3 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (31 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (19 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (9 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (3 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (28 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (38 ms)
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (140 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 14 tests from 4 test cases ran. (291 ms total)
9: [ PASSED ] 14 tests.
9/40 Test #9: FFTUnitTests ..................... Passed 0.34 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 60 tests from 19 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/0 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Swap
10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Comparison
10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Swap
10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Comparison
10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Swap
10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Comparison
10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Swap
10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Comparison
10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (1 ms total)
10:
10: [----------] 1 test from HostAllocatorUntypedTest
10: [ RUN ] HostAllocatorUntypedTest.Comparison
10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
10:
10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/2 (2 ms total)
10:
10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (1 ms)
10: [----------] 4 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 60 tests from 19 test cases ran. (10 ms total)
10: [ PASSED ] 60 tests.
10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.10 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 4 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 4 tests from HardwareTopologyTest
11: [ RUN ] HardwareTopologyTest.Execute
11: [ OK ] HardwareTopologyTest.Execute (27 ms)
11: [ RUN ] HardwareTopologyTest.HwlocExecute
11: [ OK ] HardwareTopologyTest.HwlocExecute (25 ms)
11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (27 ms)
11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (27 ms)
11: [----------] 4 tests from HardwareTopologyTest (107 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 4 tests from 1 test case ran. (107 ms total)
11: [ PASSED ] 4 tests.
11/40 Test #11: HardwareUnitTests ................ Passed 0.16 sec
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 112 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from EmptyArrayRefWithPaddingTest
12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total)
12:
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (1 ms)
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (1 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
12:
12: [----------] 6 tests from StructureSimilarityTest
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
12: [----------] 6 tests from StructureSimilarityTest (0 ms total)
12:
12: [----------] 21 tests from FunctionTest
12: [ RUN ] FunctionTest.StaticLog2
12: [ OK ] FunctionTest.StaticLog2 (1 ms)
12: [ RUN ] FunctionTest.Log2I32Bit
12: [ OK ] FunctionTest.Log2I32Bit (1 ms)
12: [ RUN ] FunctionTest.Log2I64Bit
12: [ OK ] FunctionTest.Log2I64Bit (0 ms)
12: [ RUN ] FunctionTest.GreatestCommonDivisor
12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
12: [ RUN ] FunctionTest.InvsqrtFloat
12: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
12: [ RUN ] FunctionTest.InvsqrtDouble
12: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
12: [ RUN ] FunctionTest.InvsqrtInteger
12: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
12: [ RUN ] FunctionTest.InvcbrtFloat
12: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
12: [ RUN ] FunctionTest.InvcbrtDouble
12: [ OK ] FunctionTest.InvcbrtDouble (1 ms)
12: [ RUN ] FunctionTest.InvcbrtInteger
12: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
12: [ RUN ] FunctionTest.SixthrootFloat
12: [ OK ] FunctionTest.SixthrootFloat (1 ms)
12: [ RUN ] FunctionTest.SixthrootDouble
12: [ OK ] FunctionTest.SixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.SixthrootInteger
12: [ OK ] FunctionTest.SixthrootInteger (1 ms)
12: [ RUN ] FunctionTest.InvsixthrootFloat
12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootDouble
12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootInteger
12: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
12: [ RUN ] FunctionTest.Powers
12: [ OK ] FunctionTest.Powers (0 ms)
12: [ RUN ] FunctionTest.ErfInvFloat
12: [ OK ] FunctionTest.ErfInvFloat (1 ms)
12: [ RUN ] FunctionTest.ErfInvDouble
12: [ OK ] FunctionTest.ErfInvDouble (0 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
12: [----------] 21 tests from FunctionTest (11 ms total)
12:
12: [----------] 2 tests from InvertMatrixTest
12: [ RUN ] InvertMatrixTest.IdentityIsImpotent
12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertMatrixTest.ComputesInverse
12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
12: [----------] 2 tests from InvertMatrixTest (0 ms total)
12:
12: [----------] 2 tests from InvertBoxMatrixTest
12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanCopyAssign
12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanMoveAssign
12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanSwap
12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanCopyAssign
12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanMoveAssign
12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanSwap
12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/1 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanCopyAssign
12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanMoveAssign
12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanSwap
12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanCopyAssign
12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanMoveAssign
12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanSwap
12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanCopyAssign
12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanMoveAssign
12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanSwap
12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanCopyAssign
12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanMoveAssign
12: [ OK ] PaddedVectorTest/5.CanMoveAssign (1 ms)
12: [ RUN ] PaddedVectorTest/5.CanSwap
12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/5 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanCopyAssign
12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanMoveAssign
12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanSwap
12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanCopyAssign
12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanMoveAssign
12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanSwap
12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanCopyAssign
12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanMoveAssign
12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanSwap
12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanCopyAssign
12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanMoveAssign
12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanSwap
12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total)
12:
12: [----------] 33 tests from RVecTest
12: [ RUN ] RVecTest.CanBeStoredInVector
12: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAsMutable_rvec
12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Array
12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
12: [ RUN ] RVecTest.CanAddRVecToRvec
12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanAddAssignRVecToRvec
12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractRVecFromRvec
12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanDotProductRVecByRvec
12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanCrossProductRVecByRvec
12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVecInplace
12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
12: [ RUN ] RVecTest.CanScaleRVec
12: [ OK ] RVecTest.CanScaleRVec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVec
12: [ OK ] RVecTest.CanDivideRVec (0 ms)
12: [ RUN ] RVecTest.CanDoUnitvFromRVec
12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanSqLengthOfRVec
12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanLengthOfRVec
12: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToRVec
12: [ OK ] RVecTest.CanCastToRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToDVec
12: [ OK ] RVecTest.CanCastToDVec (0 ms)
12: [ RUN ] RVecTest.CanLeftScalarMultiply
12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanRightScalarMultiply
12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanGetUnitvFromRVec
12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanGetSqLengthOfRVec
12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanGetLengthOfRVec
12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoCrossProductOfRVec
12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoDotProductOfRVec
12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
12: [ RUN ] RVecTest.WorksAs_dvec_Reference
12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_ivec_Reference
12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Reference
12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
12: [ RUN ] RVecTest.CopyConstructorWorks
12: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
12: [ RUN ] RVecTest.CopyAssignmentWorks
12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
12: [ RUN ] RVecTest.MoveConstructorWorks
12: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
12: [ RUN ] RVecTest.MoveAssignmentWorks
12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
12: [----------] 33 tests from RVecTest (1 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 112 tests from 20 test cases ran. (16 ms total)
12: [ PASSED ] 112 tests.
12/40 Test #12: MathUnitTests .................... Passed 0.08 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 17 tests from ThreadAffinityTest
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
13: NOTE: Affinity setting failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
13: NOTE: Affinity setting for 1/2 threads failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms)
13: [----------] 17 tests from ThreadAffinityTest (12 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 1 test case ran. (13 ms total)
13: [ PASSED ] 17 tests.
13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.05 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 13 tests from 2 test cases.
14: [----------] Global test environment set-up.
14: [----------] 6 tests from ThreadAffinityMultiRankTest
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (6 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (4 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (6 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (48 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (10 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (69 ms)
14: [----------] 6 tests from ThreadAffinityMultiRankTest (147 ms total)
14:
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (10 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (39 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (29 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (49 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (3 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (46 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (48 ms)
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (231 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 13 tests from 2 test cases ran. (380 ms total)
14: [ PASSED ] 13 tests.
14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.42 sec
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 22 tests from 4 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from TextTableFormatterTest
15: [ RUN ] TextTableFormatterTest.HandlesBasicCase
15: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesIndentation
15: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
15: [----------] 6 tests from TextTableFormatterTest (5 ms total)
15:
15: [----------] 3 tests from HelpManagerTest
15: [ RUN ] HelpManagerTest.HandlesRootTopic
15: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
15: [ RUN ] HelpManagerTest.HandlesSubTopics
15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
15: [ RUN ] HelpManagerTest.HandlesInvalidTopics
15: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
15: [----------] 3 tests from HelpManagerTest (2 ms total)
15:
15: [----------] 2 tests from HelpTopicFormattingTest
15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
15: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
15:
15: [----------] 11 tests from HelpWriterContextTest
15: [ RUN ] HelpWriterContextTest.FormatsParagraphs
15: [ OK ] HelpWriterContextTest.FormatsParagraphs (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralText
15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsBulletList
15: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsGridTable
15: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsTitles
15: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
15: [----------] 11 tests from HelpWriterContextTest (9 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 22 tests from 4 test cases ran. (19 ms total)
15: [ PASSED ] 22 tests.
15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.08 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 110 tests from 18 test cases.
16: [----------] Global test environment set-up.
16: [----------] 5 tests from AbstractOptionStorageTest
16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
16: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
16:
16: [----------] 8 tests from FileNameOptionTest
16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
16: [----------] 8 tests from FileNameOptionTest (2 ms total)
16:
16: [----------] 15 tests from FileNameOptionManagerTest
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
16: [----------] 15 tests from FileNameOptionManagerTest (2 ms total)
16:
16: [----------] 1 test from OptionsTest
16: [ RUN ] OptionsTest.FailsOnNonsafeStorage
16: [ OK ] OptionsTest.FailsOnNonsafeStorage (1 ms)
16: [----------] 1 test from OptionsTest (1 ms total)
16:
16: [----------] 9 tests from OptionsAssignerTest
16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMissingValue
16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesExtraValue
16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesGroups
16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesSections
16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
16: [----------] 9 tests from OptionsAssignerTest (1 ms total)
16:
16: [----------] 4 tests from OptionsAssignerBooleanTest
16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (1 ms)
16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
16: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
16:
16: [----------] 13 tests from OptionsAssignerIntegerTest
16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
16: [----------] 13 tests from OptionsAssignerIntegerTest (2 ms total)
16:
16: [----------] 5 tests from OptionsAssignerDoubleTest
16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
16:
16: [----------] 9 tests from OptionsAssignerStringTest
16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
16:
16: [----------] 6 tests from OptionsAssignerEnumTest
16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
16:
16: [----------] 8 tests from RepeatingOptionSectionTest
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
16: [----------] 8 tests from RepeatingOptionSectionTest (2 ms total)
16:
16: [----------] 1 test from TimeUnitManagerTest
16: [ RUN ] TimeUnitManagerTest.BasicOperations
16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
16: [----------] 1 test from TimeUnitManagerTest (0 ms total)
16:
16: [----------] 4 tests from TimeUnitBehaviorTest
16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
16:
16: [----------] 2 tests from TreeValueSupportAssignTest
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (1 ms)
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
16: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total)
16:
16: [----------] 1 test from TreeValueSupportAssignErrorTest
16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
16:
16: [----------] 5 tests from TreeValueSupportCheckTest
16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
16: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
16:
16: [----------] 6 tests from TreeValueSupportAdjustTest
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
16: [----------] 6 tests from TreeValueSupportAdjustTest (4 ms total)
16:
16: [----------] 8 tests from TreeValueSupportTest
16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsInt64Option
16: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsStringOption
16: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsFloatOption
16: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumOption
16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
16: [----------] 8 tests from TreeValueSupportTest (7 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 110 tests from 18 test cases ran. (30 ms total)
16: [ PASSED ] 110 tests.
16/40 Test #16: OptionsUnitTests ................. Passed 0.11 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 44 tests from 10 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from ExponentialDistributionTest
17: [ RUN ] ExponentialDistributionTest.Output
17: [ OK ] ExponentialDistributionTest.Output (55 ms)
17: [ RUN ] ExponentialDistributionTest.Logical
17: [ OK ] ExponentialDistributionTest.Logical (0 ms)
17: [ RUN ] ExponentialDistributionTest.Reset
17: [ OK ] ExponentialDistributionTest.Reset (0 ms)
17: [ RUN ] ExponentialDistributionTest.AltParam
17: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from ExponentialDistributionTest (55 ms total)
17:
17: [----------] 4 tests from GammaDistributionTest
17: [ RUN ] GammaDistributionTest.Output
17: [ OK ] GammaDistributionTest.Output (1 ms)
17: [ RUN ] GammaDistributionTest.Logical
17: [ OK ] GammaDistributionTest.Logical (0 ms)
17: [ RUN ] GammaDistributionTest.Reset
17: [ OK ] GammaDistributionTest.Reset (0 ms)
17: [ RUN ] GammaDistributionTest.AltParam
17: [ OK ] GammaDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from GammaDistributionTest (1 ms total)
17:
17: [----------] 4 tests from NormalDistributionTest
17: [ RUN ] NormalDistributionTest.Output
17: [ OK ] NormalDistributionTest.Output (1 ms)
17: [ RUN ] NormalDistributionTest.Logical
17: [ OK ] NormalDistributionTest.Logical (0 ms)
17: [ RUN ] NormalDistributionTest.Reset
17: [ OK ] NormalDistributionTest.Reset (0 ms)
17: [ RUN ] NormalDistributionTest.AltParam
17: [ OK ] NormalDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from NormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from SeedTest
17: [ RUN ] SeedTest.makeRandomSeed
17: [ OK ] SeedTest.makeRandomSeed (0 ms)
17: [----------] 1 test from SeedTest (0 ms total)
17:
17: [----------] 6 tests from TabulatedNormalDistributionTest
17: [ RUN ] TabulatedNormalDistributionTest.Output14
17: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Output16
17: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Logical
17: [ OK ] TabulatedNormalDistributionTest.Logical (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Reset
17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.AltParam
17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
17: [----------] 6 tests from TabulatedNormalDistributionTest (3 ms total)
17:
17: [----------] 1 test from TabulatedNormalDistributionTableTest
17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (10 ms)
17: [----------] 1 test from TabulatedNormalDistributionTableTest (10 ms total)
17:
17: [----------] 6 tests from ThreeFry2x64Test
17: [ RUN ] ThreeFry2x64Test.Logical
17: [ OK ] ThreeFry2x64Test.Logical (0 ms)
17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
17: [ RUN ] ThreeFry2x64Test.Reseed
17: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
17: [ RUN ] ThreeFry2x64Test.Discard
17: [ OK ] ThreeFry2x64Test.Discard (0 ms)
17: [ RUN ] ThreeFry2x64Test.InvalidCounter
17: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms)
17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
17: [----------] 6 tests from ThreeFry2x64Test (2 ms total)
17:
17: [----------] 4 tests from UniformIntDistributionTest
17: [ RUN ] UniformIntDistributionTest.Output
17: [ OK ] UniformIntDistributionTest.Output (1 ms)
17: [ RUN ] UniformIntDistributionTest.Logical
17: [ OK ] UniformIntDistributionTest.Logical (0 ms)
17: [ RUN ] UniformIntDistributionTest.Reset
17: [ OK ] UniformIntDistributionTest.Reset (0 ms)
17: [ RUN ] UniformIntDistributionTest.AltParam
17: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
17:
17: [----------] 5 tests from UniformRealDistributionTest
17: [ RUN ] UniformRealDistributionTest.GenerateCanonical
17: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
17: [ RUN ] UniformRealDistributionTest.Output
17: [ OK ] UniformRealDistributionTest.Output (1 ms)
17: [ RUN ] UniformRealDistributionTest.Logical
17: [ OK ] UniformRealDistributionTest.Logical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Reset
17: [ OK ] UniformRealDistributionTest.Reset (0 ms)
17: [ RUN ] UniformRealDistributionTest.AltParam
17: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
17: [----------] 5 tests from UniformRealDistributionTest (2 ms total)
17:
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms)
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (6 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 44 tests from 10 test cases ran. (82 ms total)
17: [ PASSED ] 44 tests.
17/40 Test #17: RandomUnitTests .................. Passed 0.18 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 1 test from 1 test case.
18: [----------] Global test environment set-up.
18: [----------] 1 test from RestraintManager
18: [ RUN ] RestraintManager.restraintList
18: [ OK ] RestraintManager.restraintList (0 ms)
18: [----------] 1 test from RestraintManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 1 test from 1 test case ran. (1 ms total)
18: [ PASSED ] 1 test.
18/40 Test #18: RestraintTests ................... Passed 0.08 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 16 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (10 ms)
19: [ RUN ] SplineTableTest/0.Sinc
19: [ OK ] SplineTableTest/0.Sinc (4 ms)
19: [ RUN ] SplineTableTest/0.LJ12
19: [ OK ] SplineTableTest/0.LJ12 (114 ms)
19: [ RUN ] SplineTableTest/0.PmeCorrection
19: [ OK ] SplineTableTest/0.PmeCorrection (7 ms)
19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms)
19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (6 ms)
19: [ RUN ] SplineTableTest/0.TwoFunctions
19: [ OK ] SplineTableTest/0.TwoFunctions (211 ms)
19: [ RUN ] SplineTableTest/0.ThreeFunctions
19: [ OK ] SplineTableTest/0.ThreeFunctions (200 ms)
19: [----------] 8 tests from SplineTableTest/0 (554 ms total)
19:
19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
19: [ RUN ] SplineTableTest/1.Sinc
19: [ OK ] SplineTableTest/1.Sinc (2 ms)
19: [ RUN ] SplineTableTest/1.LJ12
19: [ OK ] SplineTableTest/1.LJ12 (13 ms)
19: [ RUN ] SplineTableTest/1.PmeCorrection
19: [ OK ] SplineTableTest/1.PmeCorrection (5 ms)
19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (4 ms)
19: [ RUN ] SplineTableTest/1.TwoFunctions
19: [ OK ] SplineTableTest/1.TwoFunctions (31 ms)
19: [ RUN ] SplineTableTest/1.ThreeFunctions
19: [ OK ] SplineTableTest/1.ThreeFunctions (44 ms)
19: [----------] 8 tests from SplineTableTest/1 (109 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 16 tests from 2 test cases ran. (663 ms total)
19: [ PASSED ] 16 tests.
19/40 Test #19: TableUnitTests ................... Passed 0.74 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 1 test case.
20: [----------] Global test environment set-up.
20: [----------] 3 tests from GpuIdStringHandlingTest
20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork
20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (1 ms)
20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid
20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow
20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms)
20: [----------] 3 tests from GpuIdStringHandlingTest (2 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 1 test case ran. (2 ms total)
20: [ PASSED ] 3 tests.
20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.06 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 325 tests from 52 test cases.
21: [----------] Global test environment set-up.
21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.Move
21: [ OK ] AllocatorTest/0.Move (0 ms)
21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/0 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.Move
21: [ OK ] AllocatorTest/1.Move (0 ms)
21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/1 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.Move
21: [ OK ] AllocatorTest/2.Move (0 ms)
21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/2 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.Move
21: [ OK ] AllocatorTest/3.Move (0 ms)
21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/3 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.Move
21: [ OK ] AllocatorTest/4.Move (0 ms)
21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/4 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (2 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.Move
21: [ OK ] AllocatorTest/5.Move (0 ms)
21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/5 (3 ms total)
21:
21: [----------] 1 test from AllocatorUntypedTest
21: [ RUN ] AllocatorUntypedTest.Comparison
21: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
21: [----------] 1 test from AllocatorUntypedTest (0 ms total)
21:
21: [----------] 1 test from EmptyArrayRefTest
21: [ RUN ] EmptyArrayRefTest.IsEmpty
21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyArrayRefTest (0 ms total)
21:
21: [----------] 1 test from EmptyConstArrayRefTest
21: [ RUN ] EmptyConstArrayRefTest.IsEmpty
21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/1 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/2 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
21: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
21:
21: [----------] 4 tests from KeyValueTreeSerializerTest
21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
21: [----------] 4 tests from KeyValueTreeSerializerTest (4 ms total)
21:
21: [----------] 6 tests from TreeValueTransformTest
21: [ RUN ] TreeValueTransformTest.SimpleTransforms
21: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromString
21: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
21: [ RUN ] TreeValueTransformTest.ScopedTransformRules
21: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
21: [----------] 6 tests from TreeValueTransformTest (6 ms total)
21:
21: [----------] 1 test from TreeValueTransformErrorTest
21: [ RUN ] TreeValueTransformErrorTest.ConversionError
21: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
21: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
21:
21: [----------] 2 tests from RegexBasicTest
21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported
21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (2 ms)
21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported
21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (2 ms)
21: [----------] 2 tests from RegexBasicTest (4 ms total)
21:
21: [----------] 5 tests from LoggerTest
21: [ RUN ] LoggerTest.EmptyLoggerWorks
21: [ OK ] LoggerTest.EmptyLoggerWorks (1 ms)
21: [ RUN ] LoggerTest.LogsToStream
21: [ OK ] LoggerTest.LogsToStream (0 ms)
21: [ RUN ] LoggerTest.LogsToFile
21: [ OK ] LoggerTest.LogsToFile (2 ms)
21: [ RUN ] LoggerTest.LevelFilteringWorks
21: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
21: [ RUN ] LoggerTest.LogsToMultipleStreams
21: [ OK ] LoggerTest.LogsToMultipleStreams (1 ms)
21: [----------] 5 tests from LoggerTest (5 ms total)
21:
21: [----------] 4 tests from MutexBasicTest
21: [ RUN ] MutexBasicTest.CanBeMade
21: [ OK ] MutexBasicTest.CanBeMade (0 ms)
21: [ RUN ] MutexBasicTest.CanBeLocked
21: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeTryLocked
21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
21: [----------] 4 tests from MutexBasicTest (0 ms total)
21:
21: [----------] 3 tests from MutexTaskTest
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
21: [----------] 3 tests from MutexTaskTest (2 ms total)
21:
21: [----------] 4 tests from PathTest
21: [ RUN ] PathTest.StripSourcePrefixWorks
21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks
21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathWorks
21: [ OK ] PathTest.GetParentPathWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathAndBasenameWorks
21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms)
21: [----------] 4 tests from PathTest (0 ms total)
21:
21: [----------] 2 tests from PhysicalNodeCommunicatorTest
21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
21:
21: [----------] 7 tests from StringUtilityTest
21: [ RUN ] StringUtilityTest.StartsWith
21: [ OK ] StringUtilityTest.StartsWith (0 ms)
21: [ RUN ] StringUtilityTest.EndsWith
21: [ OK ] StringUtilityTest.EndsWith (0 ms)
21: [ RUN ] StringUtilityTest.StripSuffixIfPresent
21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
21: [ RUN ] StringUtilityTest.StripString
21: [ OK ] StringUtilityTest.StripString (0 ms)
21: [ RUN ] StringUtilityTest.SplitString
21: [ OK ] StringUtilityTest.SplitString (1 ms)
21: [ RUN ] StringUtilityTest.SplitDelimitedString
21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (2 ms)
21: [----------] 7 tests from StringUtilityTest (3 ms total)
21:
21: [----------] 2 tests from FormatStringTest
21: [ RUN ] FormatStringTest.HandlesBasicFormatting
21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
21: [ RUN ] FormatStringTest.HandlesLongStrings
21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
21: [----------] 2 tests from FormatStringTest (0 ms total)
21:
21: [----------] 1 test from StringFormatterTest
21: [ RUN ] StringFormatterTest.HandlesBasicFormatting
21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
21: [----------] 1 test from StringFormatterTest (0 ms total)
21:
21: [----------] 1 test from formatAndJoinTest
21: [ RUN ] formatAndJoinTest.Works
21: [ OK ] formatAndJoinTest.Works (0 ms)
21: [----------] 1 test from formatAndJoinTest (0 ms total)
21:
21: [----------] 1 test from JoinStringsTest
21: [ RUN ] JoinStringsTest.Works
21: [ OK ] JoinStringsTest.Works (0 ms)
21: [----------] 1 test from JoinStringsTest (0 ms total)
21:
21: [----------] 6 tests from ReplaceAllTest
21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesNoMatches
21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
21: [----------] 6 tests from ReplaceAllTest (0 ms total)
21:
21: [----------] 10 tests from TextLineWrapperTest
21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectly
21: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndent
21: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
21: [----------] 10 tests from TextLineWrapperTest (6 ms total)
21:
21: [----------] 6 tests from TextWriterTest
21: [ RUN ] TextWriterTest.WritesLines
21: [ OK ] TextWriterTest.WritesLines (1 ms)
21: [ RUN ] TextWriterTest.WritesLinesInParts
21: [ OK ] TextWriterTest.WritesLinesInParts (1 ms)
21: [ RUN ] TextWriterTest.WritesWrappedLines
21: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms)
21: [ RUN ] TextWriterTest.TracksNewlines
21: [ OK ] TextWriterTest.TracksNewlines (0 ms)
21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
21: [----------] 6 tests from TextWriterTest (4 ms total)
21:
21: [----------] 1 test from TypeTraitsTest
21: [ RUN ] TypeTraitsTest.IsIntegralConstant
21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
21: [----------] 1 test from TypeTraitsTest (0 ms total)
21:
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
21:
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (1 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
21:
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
21:
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (4 ms total)
21:
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 325 tests from 52 test cases ran. (72 ms total)
21: [ PASSED ] 325 tests.
21/40 Test #21: UtilityUnitTests ................. Passed 0.18 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 2 tests from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from PhysicalNodeCommunicatorTest
22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms)
22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (11 ms)
22: [----------] 2 tests from PhysicalNodeCommunicatorTest (14 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 2 tests from 1 test case ran. (14 ms total)
22: [ PASSED ] 2 tests.
22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.06 sec
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 17 tests from 4 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from FileMD5Test
23: [ RUN ] FileMD5Test.CanComputeMD5
23: [ OK ] FileMD5Test.CanComputeMD5 (8 ms)
23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
23: [----------] 2 tests from FileMD5Test (9 ms total)
23:
23: [----------] 9 tests from ReadTest
23: [ RUN ] ReadTest.get_eint_ReadsInteger
23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_eint64_ReadsInteger
23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsInteger
23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsFloat
23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
23: [ RUN ] ReadTest.get_ereal_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not a
23: real value
23:
23:
23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
23: [----------] 9 tests from ReadTest (1 ms total)
23:
23: [----------] 2 tests from TngTest
23: [ RUN ] TngTest.CanOpenTngFile
23: [ OK ] TngTest.CanOpenTngFile (1 ms)
23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
23: [----------] 2 tests from TngTest (1 ms total)
23:
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (4 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (73 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (83 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 17 tests from 4 test cases ran. (94 ms total)
23: [ PASSED ] 17 tests.
23/40 Test #23: FileIOTests ...................... Passed 0.15 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 5 tests from 1 test case.
24: [----------] Global test environment set-up.
24: [----------] 5 tests from PullTest
24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (1 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
24: [----------] 5 tests from PullTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 5 tests from 1 test case ran. (1 ms total)
24: [ PASSED ] 5 tests.
24/40 Test #24: PullTest ......................... Passed 0.06 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 12 tests from 4 test cases.
25: [----------] Global test environment set-up.
25: [----------] 1 test from BiasTest
25: [ RUN ] BiasTest.DetectsCovering
25: [ OK ] BiasTest.DetectsCovering (4 ms)
25: [----------] 1 test from BiasTest (4 ms total)
25:
25: [----------] 1 test from gridTest
25: [ RUN ] gridTest.neighborhood
25: [ OK ] gridTest.neighborhood (8 ms)
25: [----------] 1 test from gridTest (8 ms total)
25:
25: [----------] 8 tests from WithParameters/BiasTest
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (12 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms)
25: [----------] 8 tests from WithParameters/BiasTest (34 ms total)
25:
25: [----------] 2 tests from WithParameters/BiasStateTest
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (2 ms)
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
25: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 12 tests from 4 test cases ran. (50 ms total)
25: [ PASSED ] 12 tests.
25/40 Test #25: AwhTest .......................... Passed 0.11 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 86 tests from 3 test cases.
26: [----------] Global test environment set-up.
26: [----------] 41 tests from SimdScalarTest
26: [ RUN ] SimdScalarTest.load
26: [ OK ] SimdScalarTest.load (0 ms)
26: [ RUN ] SimdScalarTest.loadU
26: [ OK ] SimdScalarTest.loadU (0 ms)
26: [ RUN ] SimdScalarTest.store
26: [ OK ] SimdScalarTest.store (0 ms)
26: [ RUN ] SimdScalarTest.storeU
26: [ OK ] SimdScalarTest.storeU (0 ms)
26: [ RUN ] SimdScalarTest.setZero
26: [ OK ] SimdScalarTest.setZero (0 ms)
26: [ RUN ] SimdScalarTest.andNot
26: [ OK ] SimdScalarTest.andNot (0 ms)
26: [ RUN ] SimdScalarTest.fma
26: [ OK ] SimdScalarTest.fma (0 ms)
26: [ RUN ] SimdScalarTest.fms
26: [ OK ] SimdScalarTest.fms (0 ms)
26: [ RUN ] SimdScalarTest.fnma
26: [ OK ] SimdScalarTest.fnma (0 ms)
26: [ RUN ] SimdScalarTest.fnms
26: [ OK ] SimdScalarTest.fnms (0 ms)
26: [ RUN ] SimdScalarTest.maskAdd
26: [ OK ] SimdScalarTest.maskAdd (0 ms)
26: [ RUN ] SimdScalarTest.maskzMul
26: [ OK ] SimdScalarTest.maskzMul (0 ms)
26: [ RUN ] SimdScalarTest.maskzFma
26: [ OK ] SimdScalarTest.maskzFma (0 ms)
26: [ RUN ] SimdScalarTest.abs
26: [ OK ] SimdScalarTest.abs (0 ms)
26: [ RUN ] SimdScalarTest.max
26: [ OK ] SimdScalarTest.max (0 ms)
26: [ RUN ] SimdScalarTest.min
26: [ OK ] SimdScalarTest.min (0 ms)
26: [ RUN ] SimdScalarTest.round
26: [ OK ] SimdScalarTest.round (0 ms)
26: [ RUN ] SimdScalarTest.trunc
26: [ OK ] SimdScalarTest.trunc (0 ms)
26: [ RUN ] SimdScalarTest.reduce
26: [ OK ] SimdScalarTest.reduce (0 ms)
26: [ RUN ] SimdScalarTest.testBits
26: [ OK ] SimdScalarTest.testBits (0 ms)
26: [ RUN ] SimdScalarTest.anyTrue
26: [ OK ] SimdScalarTest.anyTrue (0 ms)
26: [ RUN ] SimdScalarTest.selectByMask
26: [ OK ] SimdScalarTest.selectByMask (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMask
26: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
26: [ RUN ] SimdScalarTest.blend
26: [ OK ] SimdScalarTest.blend (0 ms)
26: [ RUN ] SimdScalarTest.cvtR2I
26: [ OK ] SimdScalarTest.cvtR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvttR2I
26: [ OK ] SimdScalarTest.cvttR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvtI2R
26: [ OK ] SimdScalarTest.cvtI2R (0 ms)
26: [ RUN ] SimdScalarTest.cvtF2D
26: [ OK ] SimdScalarTest.cvtF2D (0 ms)
26: [ RUN ] SimdScalarTest.cvtD2D
26: [ OK ] SimdScalarTest.cvtD2D (0 ms)
26: [ RUN ] SimdScalarTest.loadI
26: [ OK ] SimdScalarTest.loadI (0 ms)
26: [ RUN ] SimdScalarTest.loadUI
26: [ OK ] SimdScalarTest.loadUI (0 ms)
26: [ RUN ] SimdScalarTest.storeI
26: [ OK ] SimdScalarTest.storeI (0 ms)
26: [ RUN ] SimdScalarTest.storeUI
26: [ OK ] SimdScalarTest.storeUI (0 ms)
26: [ RUN ] SimdScalarTest.andNotI
26: [ OK ] SimdScalarTest.andNotI (0 ms)
26: [ RUN ] SimdScalarTest.testBitsI
26: [ OK ] SimdScalarTest.testBitsI (0 ms)
26: [ RUN ] SimdScalarTest.selectByMaskI
26: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMaskI
26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
26: [ RUN ] SimdScalarTest.blendI
26: [ OK ] SimdScalarTest.blendI (0 ms)
26: [ RUN ] SimdScalarTest.cvtB2IB
26: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
26: [ RUN ] SimdScalarTest.cvtIB2B
26: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
26: [ RUN ] SimdScalarTest.expandScalarsToTriplets
26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
26: [----------] 41 tests from SimdScalarTest (2 ms total)
26:
26: [----------] 8 tests from SimdScalarUtilTest
26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
26: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
26:
26: [----------] 37 tests from SimdScalarMathTest
26: [ RUN ] SimdScalarMathTest.copysign
26: [ OK ] SimdScalarMathTest.copysign (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPair
26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
26: [ RUN ] SimdScalarMathTest.inv
26: [ OK ] SimdScalarMathTest.inv (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrt
26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
26: [ RUN ] SimdScalarMathTest.log
26: [ OK ] SimdScalarMathTest.log (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2
26: [ OK ] SimdScalarMathTest.exp2 (0 ms)
26: [ RUN ] SimdScalarMathTest.exp
26: [ OK ] SimdScalarMathTest.exp (0 ms)
26: [ RUN ] SimdScalarMathTest.erf
26: [ OK ] SimdScalarMathTest.erf (0 ms)
26: [ RUN ] SimdScalarMathTest.erfc
26: [ OK ] SimdScalarMathTest.erfc (0 ms)
26: [ RUN ] SimdScalarMathTest.sincos
26: [ OK ] SimdScalarMathTest.sincos (0 ms)
26: [ RUN ] SimdScalarMathTest.sin
26: [ OK ] SimdScalarMathTest.sin (0 ms)
26: [ RUN ] SimdScalarMathTest.cos
26: [ OK ] SimdScalarMathTest.cos (0 ms)
26: [ RUN ] SimdScalarMathTest.tan
26: [ OK ] SimdScalarMathTest.tan (0 ms)
26: [ RUN ] SimdScalarMathTest.asin
26: [ OK ] SimdScalarMathTest.asin (0 ms)
26: [ RUN ] SimdScalarMathTest.acos
26: [ OK ] SimdScalarMathTest.acos (0 ms)
26: [ RUN ] SimdScalarMathTest.atan
26: [ OK ] SimdScalarMathTest.atan (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2
26: [ OK ] SimdScalarMathTest.atan2 (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrection
26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.invSingleAccuracy
26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.logSingleAccuracy
26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.expSingleAccuracy
26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
26: [----------] 37 tests from SimdScalarMathTest (2 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 86 tests from 3 test cases ran. (5 ms total)
26: [ PASSED ] 86 tests.
26/40 Test #26: SimdUnitTests .................... Passed 0.06 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 6 tests from 6 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from CompatibilityHelper
27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles
27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms)
27: [----------] 1 test from CompatibilityHelper (0 ms total)
27:
27: [----------] 1 test from NotNullConstruction
27: [ RUN ] NotNullConstruction.Works
27: [ OK ] NotNullConstruction.Works (0 ms)
27: [----------] 1 test from NotNullConstruction (0 ms total)
27:
27: [----------] 1 test from NotNullCasting
27: [ RUN ] NotNullCasting.Works
27: [ OK ] NotNullCasting.Works (0 ms)
27: [----------] 1 test from NotNullCasting (0 ms total)
27:
27: [----------] 1 test from NotNullAssignment
27: [ RUN ] NotNullAssignment.Works
27: [ OK ] NotNullAssignment.Works (0 ms)
27: [----------] 1 test from NotNullAssignment (0 ms total)
27:
27: [----------] 1 test from MakeNotNull
27: [ RUN ] MakeNotNull.Works
27: [ OK ] MakeNotNull.Works (0 ms)
27: [----------] 1 test from MakeNotNull (0 ms total)
27:
27: [----------] 1 test from NotNull
27: [ RUN ] NotNull.WorksInContainers
27: [ OK ] NotNull.WorksInContainers (0 ms)
27: [----------] 1 test from NotNull (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 6 tests from 6 test cases ran. (1 ms total)
27: [ PASSED ] 6 tests.
27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.04 sec
test 28
Start 28: GmxAnaTest
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
28: Test timeout computed to be: 600
28: [==========] Running 26 tests from 5 test cases.
28: [----------] Global test environment set-up.
28: [----------] 5 tests from Entropy
28: [ RUN ] Entropy.Schlitter_300_NoLinear
28: [ OK ] Entropy.Schlitter_300_NoLinear (13 ms)
28: [ RUN ] Entropy.Schlitter_300_Linear
28: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (1 ms)
28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_200_Linear
28: [ OK ] Entropy.QuasiHarmonic_200_Linear (1 ms)
28: [----------] 5 tests from Entropy (15 ms total)
28:
28: [----------] 3 tests from MsdTest
28: [ RUN ] MsdTest.threeDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.threeDimensionalDiffusion (7 ms)
28: [ RUN ] MsdTest.twoDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.twoDimensionalDiffusion (5 ms)
28: [ RUN ] MsdTest.oneDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.oneDimensionalDiffusion (4 ms)
28: [----------] 3 tests from MsdTest (16 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: trr version: GMX_trn_file (single precision)
28:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (10 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (10 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (9 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (56 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (28 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (18 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (18 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (19 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm)
28: -> frame 0 time 0.000
't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (19 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (18 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (120 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (3 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm)
28: -> frame 0 time 0.000
't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (5 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (28 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 26 tests from 5 test cases ran. (236 ms total)
28: [ PASSED ] 26 tests.
28/40 Test #28: GmxAnaTest ....................... Passed 0.29 sec
test 29
Start 29: GmxPreprocessTests
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 26 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 4 tests from GenconfTest
29: [ RUN ] GenconfTest.nbox_Works
29: [ OK ] GenconfTest.nbox_Works (7 ms)
29: [ RUN ] GenconfTest.nbox_norenumber_Works
29: [ OK ] GenconfTest.nbox_norenumber_Works (5 ms)
29: [ RUN ] GenconfTest.nbox_dist_Works
29: [ OK ] GenconfTest.nbox_dist_Works (26 ms)
29: [ RUN ] GenconfTest.nbox_rot_Works
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: [ OK ] GenconfTest.nbox_rot_Works (8 ms)
29: [----------] 4 tests from GenconfTest (46 ms total)
29:
29: [----------] 5 tests from InsertMoleculesTest
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 8 atoms)!
29:
29: Added 1 molecules (out of 1 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
29:
29: Output configuration contains 8 atoms in 4 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (20 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 2 atoms)!
29:
Try 2 success (now 4 atoms)!
29:
Try 3 success (now 6 atoms)!
29:
Try 4 success (now 8 atoms)!
29:
Try 5 success (now 10 atoms)!
29:
29: Added 5 molecules (out of 5 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
29:
29: Output configuration contains 10 atoms in 10 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (9 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 8 atoms)!
29:
Try 2 success (now 10 atoms)!
29:
29: Added 2 molecules (out of 2 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
29:
29: Output configuration contains 10 atoms in 4 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (10 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 650 atoms)!
29:
Try 2 success (now 652 atoms)!
29:
Try 3 success (now 654 atoms)!
29:
Try 4 success (now 656 atoms)!
29:
29: Added 4 molecules (out of 4 requested)
29: Replaced 8 residues (24 atoms)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
29:
29: Output configuration contains 632 atoms in 212 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (56 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
29:
29:
Try 1 success (now 2 atoms)!
29:
Try 2 success (now 4 atoms)!
29:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
29:
Try 13 success (now 6 atoms)!
29:
29: Added 3 molecules (out of 4 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
29:
29: Output configuration contains 6 atoms in 3 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (10 ms)
29: [----------] 5 tests from InsertMoleculesTest (105 ms total)
29:
29: [----------] 12 tests from GetIrTest
29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: Ignoring obsolete mdp entry 'title'
29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (19 ms)
29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme
29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (15 ms)
29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (19 ms)
29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (33 ms)
29: [ RUN ] GetIrTest.EmptyInputWorks
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.EmptyInputWorks (16 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricField
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricField (15 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (18 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (19 ms)
29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys
29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (11 ms)
29: [ RUN ] GetIrTest.ImplicitSolventNoWorks
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ImplicitSolventNoWorks (23 ms)
29: [ RUN ] GetIrTest.ImplicitSolventYesWorks
29: [ OK ] GetIrTest.ImplicitSolventYesWorks (23 ms)
29: [ RUN ] GetIrTest.HandlesMimic
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]:
29: /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.HandlesMimic (16 ms)
29: [----------] 12 tests from GetIrTest (228 ms total)
29:
29: [----------] 5 tests from SolvateTest
29: [ RUN ] SolvateTest.cs_box_Works
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 1x1x1 boxes
29: Solvent box contains 270 atoms in 90 residues
29: Removed 129 solvent atoms due to solvent-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 47 residues
29: Generated solvent containing 141 atoms in 47 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
29:
29: Output configuration contains 141 atoms in 47 residues
29: Volume : 1.331 (nm^3)
29: Density : 1056.36 (g/l)
29: Number of solvent molecules: 47
29:
29: [ OK ] SolvateTest.cs_box_Works (88 ms)
29: [ RUN ] SolvateTest.cs_cp_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 886 residues
29: Generated solvent containing 2658 atoms in 886 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
29:
29: Output configuration contains 2664 atoms in 888 residues
29: Volume : 27.2709 (nm^3)
29: Density : 974.777 (g/l)
29: Number of solvent molecules: 886
29:
29: [ OK ] SolvateTest.cs_cp_Works (199 ms)
29: [ RUN ] SolvateTest.cs_cp_p_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 886 residues
29: Generated solvent containing 2658 atoms in 886 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
29:
29: Output configuration contains 2664 atoms in 888 residues
29: Volume : 27.2709 (nm^3)
29: Density : 974.777 (g/l)
29: Number of solvent molecules: 886
29:
29: Processing topology
29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top)
29: [ OK ] SolvateTest.cs_cp_p_Works (224 ms)
29: [ RUN ] SolvateTest.shell_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 1902 solvent atoms more than 1.000000 nm from solute.
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 252 residues
29: Generated solvent containing 756 atoms in 252 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
29:
29: Output configuration contains 762 atoms in 254 residues
29: Volume : 27.2709 (nm^3)
29: Density : 279.3 (g/l)
29: Number of solvent molecules: 252
29:
29: [ OK ] SolvateTest.shell_Works (91 ms)
29: [ RUN ] SolvateTest.update_Topology_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 3x3x3 boxes
29: Solvent box contains 14952 atoms in 4984 residues
29: Removed 2787 solvent atoms due to solvent-solvent overlap
29: Removed 30 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 2 different molecule types:
29: HOH ( 3 atoms): 1876 residues
29: SOL ( 3 atoms): 2169 residues
29: Generated solvent containing 0 atoms in 0 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
29:
29: Output configuration contains 12141 atoms in 4047 residues
29: Volume : 125 (nm^3)
29: Density : 968.963 (g/l)
29: Number of solvent molecules: 4045
29:
29: Processing topology
29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
29: [ OK ] SolvateTest.update_Topology_Works (869 ms)
29: [----------] 5 tests from SolvateTest (1472 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 26 tests from 4 test cases ran. (1851 ms total)
29: [ PASSED ] 26 tests.
29/40 Test #29: GmxPreprocessTests ............... Passed 1.92 sec
test 30
Start 30: Pdb2gmxTest
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmxTest.xml"
30: Test timeout computed to be: 480
30: [==========] Running 80 tests from 6 test cases.
30: [----------] Global test environment set-up.
30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
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Atomtype 241
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Atomtype 366
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Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
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Atomtype 386
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Atomtype 426
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Atomtype 567
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Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
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Atomtype 580
Atomtype 581
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Atomtype 641
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Atomtype 791
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Atomtype 793
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Atomtype 795
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Atomtype 797
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Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
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Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (2222 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
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Atomtype 13
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Atomtype 17
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Atomtype 24
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Atomtype 30
Atomtype 31
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Atomtype 33
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Atomtype 37
Atomtype 38
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Atomtype 41
Atomtype 42
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Atomtype 51
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Atomtype 53
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Atomtype 56
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Atomtype 122
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Atomtype 125
Atomtype 126
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Atomtype 131
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Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
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Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
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Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
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Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
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Atomtype 184
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Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
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Atomtype 199
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Atomtype 201
Atomtype 202
Atomtype 203
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Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
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Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
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Atomtype 259
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Atomtype 261
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Atomtype 264
Atomtype 265
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Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
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Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
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Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (2291 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (2137 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (1890 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
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Atomtype 640
Atomtype 641
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Atomtype 789
Atomtype 790
Atomtype 791
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Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
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Atomtype 810
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Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (2099 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
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Atomtype 59
Atomtype 60
Atomtype 61
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Atomtype 135
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Atomtype 137
Atomtype 138
Atomtype 139
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Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
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Atomtype 148
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Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
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Atomtype 160
Atomtype 161
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Atomtype 164
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Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
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Atomtype 173
Atomtype 174
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Atomtype 176
Atomtype 177
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Atomtype 179
Atomtype 180
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Atomtype 183
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Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
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Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
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Atomtype 247
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Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
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Atomtype 261
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Atomtype 267
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Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
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Atomtype 276
Atomtype 277
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Atomtype 280
Atomtype 281
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Atomtype 283
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Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (2402 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (2214 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (1974 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (1859 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
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Atomtype 174
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Atomtype 176
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Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
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Atomtype 205
Atomtype 206
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Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
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Atomtype 675
Atomtype 676
Atomtype 677
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Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
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Atomtype 686
Atomtype 687
Atomtype 688
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Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
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Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (2079 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (1839 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (1724 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (1769 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
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Atomtype 42
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Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
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Atomtype 71
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Atomtype 136
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Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
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Atomtype 196
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Atomtype 200
Atomtype 201
Atomtype 202
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Atomtype 216
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Atomtype 220
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Atomtype 223
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Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
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Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
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Atomtype 258
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Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
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Atomtype 287
Atomtype 288
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Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
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Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
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Atomtype 360
Atomtype 361
Atomtype 362
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Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
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Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
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Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
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Atomtype 409
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Atomtype 421
Atomtype 422
Atomtype 423
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Atomtype 426
Atomtype 427
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Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
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Atomtype 436
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Atomtype 438
Atomtype 439
Atomtype 440
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Atomtype 442
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Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
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Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
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Atomtype 464
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Atomtype 469
Atomtype 470
Atomtype 471
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Atomtype 500
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Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
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Atomtype 511
Atomtype 512
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Atomtype 515
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Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
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Atomtype 523
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Atomtype 539
Atomtype 540
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Atomtype 553
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Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
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Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
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Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
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Atomtype 610
Atomtype 611
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Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
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Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
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Atomtype 660
Atomtype 661
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Atomtype 665
Atomtype 666
Atomtype 667
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Atomtype 680
Atomtype 681
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Atomtype 694
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Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
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Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
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Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
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Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (2207 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (1967 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (1727 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (1767 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (2173 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
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Atomtype 223
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Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
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Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
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Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
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Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
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Atomtype 281
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Atomtype 292
Atomtype 293
Atomtype 294
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Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
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Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
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Atomtype 480
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Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
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Atomtype 487
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Atomtype 491
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Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
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Atomtype 518
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Atomtype 520
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Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
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Atomtype 532
Atomtype 533
Atomtype 534
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Atomtype 536
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Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
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Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
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Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
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Atomtype 608
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Atomtype 610
Atomtype 611
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Atomtype 614
Atomtype 615
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Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
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Atomtype 700
Atomtype 701
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Atomtype 703
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Atomtype 711
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Atomtype 713
Atomtype 714
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Atomtype 728
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Atomtype 737
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Atomtype 745
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Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
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Atomtype 767
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Atomtype 769
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Atomtype 771
Atomtype 772
Atomtype 773
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Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (1812 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
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Atomtype 65
Atomtype 66
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Atomtype 68
Atomtype 69
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Atomtype 71
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Atomtype 73
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Atomtype 79
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Atomtype 93
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Atomtype 95
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Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
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Atomtype 105
Atomtype 106
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Atomtype 109
Atomtype 110
Atomtype 111
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Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (1696 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (2260 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (2516 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
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Atomtype 48
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Atomtype 52
Atomtype 53
Atomtype 54
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Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
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Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
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Atomtype 254
Atomtype 255
Atomtype 256
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Atomtype 261
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Atomtype 264
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Atomtype 269
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Atomtype 314
Atomtype 315
Atomtype 316
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Atomtype 325
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Atomtype 327
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Atomtype 329
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Atomtype 337
Atomtype 338
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Atomtype 367
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Atomtype 386
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Atomtype 426
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Atomtype 436
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Atomtype 440
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Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
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Atomtype 459
Atomtype 460
Atomtype 461
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Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
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Atomtype 516
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Atomtype 560
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Atomtype 562
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Atomtype 564
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Atomtype 566
Atomtype 567
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Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
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Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
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Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
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Atomtype 619
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Atomtype 621
Atomtype 622
Atomtype 623
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Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
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Atomtype 650
Atomtype 651
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Atomtype 700
Atomtype 701
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Atomtype 703
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Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
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Atomtype 728
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Atomtype 737
Atomtype 738
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Atomtype 741
Atomtype 742
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Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
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Atomtype 763
Atomtype 764
Atomtype 765
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Atomtype 767
Atomtype 768
Atomtype 769
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Atomtype 771
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Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (2066 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
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Atomtype 97
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Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
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Atomtype 106
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Atomtype 111
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Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (1867 ms)
30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (48589 ms total)
30:
30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (1022 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (904 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (877 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (826 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Marked 37 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 37 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (989 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Marked 53 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 51 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (1066 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Marked 36 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 36 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (918 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Marked 33 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 31 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (920 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (913 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (1022 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (874 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (844 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Marked 37 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 37 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (1026 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Marked 53 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 51 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (1125 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Marked 36 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 36 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (969 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Marked 33 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 31 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (838 ms)
30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (15140 ms total)
30:
30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (1082 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (1079 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (913 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (948 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Marked 39 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 39 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (1028 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Marked 57 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 55 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (1192 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Marked 38 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 38 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (1004 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Marked 35 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 33 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (947 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (977 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (1093 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (998 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (948 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Marked 39 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 39 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (970 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Marked 57 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 55 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (1189 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Marked 38 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 38 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (1013 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Marked 35 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 33 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (904 ms)
30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (16287 ms total)
30:
30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 255, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 691 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 691 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.132 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (1690 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 291, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 788 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 788 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.366 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (1868 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 262, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 727 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 727 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.124 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (1583 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 233, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 634 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 634 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.888 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (1571 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 255, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 691 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 691 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.132 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (1784 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 291, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 788 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 788 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.366 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (1977 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 262, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 727 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 727 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.124 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (1842 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 233, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 634 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 634 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.888 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (1648 ms)
30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (13964 ms total)
30:
30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 663 dihedrals, 48 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.115 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (1770 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 778 dihedrals, 49 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (1958 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 696 dihedrals, 39 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.130 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (1662 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 618 dihedrals, 38 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.885 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (1445 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 663 dihedrals, 48 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.115 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (1682 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 778 dihedrals, 49 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (2024 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 696 dihedrals, 39 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.130 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (1846 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 618 dihedrals, 38 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.885 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (1659 ms)
30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (14048 ms total)
30:
30: [----------] 8 tests from ChainSep/Pdb2gmxTest
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 258, now 258
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 651 pairs
30: Before cleaning: 661 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 10 cmap torsion pairs
30: There are 661 dihedrals, 46 impropers, 463 angles
30: 648 pairs, 258 bonds and 0 virtual sites
30: Total mass 1882.146 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on changing chain id only (ignoring TER records).
30:
30: Merged chains into joint molecule definitions at 2 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Identified residue PHE6 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Start terminus PHE-6: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 258 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (1635 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 50, now 50
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 123 pairs
30: Before cleaning: 123 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 123 dihedrals, 9 impropers, 88 angles
30: 123 pairs, 50 bonds and 0 virtual sites
30: Total mass 434.421 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 10 donors and 7 acceptors were found.
30: There are 7 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS8
30: NE223
30: MET12 SD55 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 125, now 125
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 317 pairs
30: Before cleaning: 322 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 5 cmap torsion pairs
30: There are 322 dihedrals, 19 impropers, 227 angles
30: 314 pairs, 125 bonds and 0 virtual sites
30: Total mass 846.083 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 258 atoms and 16 residues
30: Total mass in system 1882.146 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on changing chain id only (ignoring TER records).
30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 4 28
30: 2 'B' 7 58
30: 3 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (28 atoms, 4 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 51 atoms
30: Chain time...
30: Processing chain 2 'B' (58 atoms, 7 residues)
30: Identified residue PHE6 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus PHE-6: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 7 residues with 124 atoms
30: Chain time...
30: Processing chain 3 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 51 atoms 4 residues
30: Including chain 2 in system: 124 atoms 7 residues
30: Including chain 3 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (220 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 258, now 258
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 651 pairs
30: Before cleaning: 661 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 10 cmap torsion pairs
30: There are 661 dihedrals, 46 impropers, 463 angles
30: 648 pairs, 258 bonds and 0 virtual sites
30: Total mass 1882.146 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records only (ignoring chain id).
30:
30: Merged chains into joint molecule definitions at 2 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus ILE-9: COO-
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 258 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (1695 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 10 donors and 12 acceptors were found.
30: There are 13 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3
30: SG9
30: HIS8 NE251 1.055
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 115, now 115
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 288 pairs
30: Before cleaning: 293 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 6 cmap torsion pairs
30: There are 293 dihedrals, 23 impropers, 203 angles
30: 285 pairs, 115 bonds and 0 virtual sites
30: Total mass 888.952 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 60, now 60
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 152 pairs
30: Before cleaning: 152 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 1 cmap torsion pairs
30: There are 152 dihedrals, 5 impropers, 112 angles
30: 152 pairs, 60 bonds and 0 virtual sites
30: Total mass 391.552 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 258 atoms and 16 residues
30: Total mass in system 1882.146 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records only (ignoring chain id).
30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 8 61
30: 2 'B' 3 25
30: 3 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (61 atoms, 8 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus ILE-9: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 8 residues with 114 atoms
30: Chain time...
30: Processing chain 2 'B' (25 atoms, 3 residues)
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 3 residues with 61 atoms
30: Chain time...
30: Processing chain 3 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 114 atoms 8 residues
30: Including chain 2 in system: 61 atoms 3 residues
30: Including chain 3 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (219 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 260, now 260
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 650 pairs
30: Before cleaning: 660 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 8 cmap torsion pairs
30: There are 660 dihedrals, 45 impropers, 466 angles
30: 647 pairs, 260 bonds and 0 virtual sites
30: Total mass 1900.162 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30:
30: Merged chains into joint molecule definitions at 3 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Identified residue PHE6 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Start terminus PHE-6: NH3+
30: End terminus ILE-9: COO-
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 261 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (1558 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 50, now 50
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 123 pairs
30: Before cleaning: 123 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 123 dihedrals, 9 impropers, 88 angles
30: 123 pairs, 50 bonds and 0 virtual sites
30: Total mass 434.421 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 6 donors and 4 acceptors were found.
30: There are 3 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 67, now 67
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 164 pairs
30: Before cleaning: 169 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 169 dihedrals, 13 impropers, 118 angles
30: 161 pairs, 67 bonds and 0 virtual sites
30: Total mass 472.547 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 60, now 60
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 152 pairs
30: Before cleaning: 152 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 1 cmap torsion pairs
30: There are 152 dihedrals, 5 impropers, 112 angles
30: 152 pairs, 60 bonds and 0 virtual sites
30: Total mass 391.552 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 261 atoms and 16 residues
30: Total mass in system 1900.162 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
30: They will be treated as separate chains unless you reorder your file.
30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 4 28
30: 2 'B' 4 33
30: 3 'B' 3 25
30: 4 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (28 atoms, 4 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 51 atoms
30: Chain time...
30: Processing chain 2 'B' (33 atoms, 4 residues)
30: Identified residue PHE6 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Start terminus PHE-6: NH3+
30: End terminus ILE-9: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 66 atoms
30: Chain time...
30: Processing chain 3 'B' (25 atoms, 3 residues)
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 3 residues with 61 atoms
30: Chain time...
30: Processing chain 4 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 51 atoms 4 residues
30: Including chain 2 in system: 66 atoms 4 residues
30: Including chain 3 in system: 61 atoms 3 residues
30: Including chain 4 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (228 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 256, now 256
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 652 pairs
30: Before cleaning: 662 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 12 cmap torsion pairs
30: There are 662 dihedrals, 47 impropers, 460 angles
30: 649 pairs, 256 bonds and 0 virtual sites
30: Total mass 1864.131 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records and chain id changing.
30:
30: Merged chains into joint molecule definitions at 1 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (1662 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 14 donors and 15 acceptors were found.
30: There are 20 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 173, now 173
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 441 pairs
30: Before cleaning: 446 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 9 cmap torsion pairs
30: There are 446 dihedrals, 29 impropers, 312 angles
30: 438 pairs, 173 bonds and 0 virtual sites
30: Total mass 1262.488 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 255 atoms and 16 residues
30: Total mass in system 1864.131 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records and chain id changing.
30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 11 86
30: 2 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (86 atoms, 11 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 11 residues with 172 atoms
30: Chain time...
30: Processing chain 2 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 172 atoms 11 residues
30: Including chain 2 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (234 ms)
30: [----------] 8 tests from ChainSep/Pdb2gmxTest (7452 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 80 tests from 6 test cases ran. (115482 ms total)
30: [ PASSED ] 80 tests.
30/40 Test #30: Pdb2gmxTest ...................... Passed 115.56 sec
test 31
Start 31: CorrelationsTest
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 11 tests from 2 test cases.
31: [----------] Global test environment set-up.
31: [----------] 10 tests from AutocorrTest
31: [ RUN ] AutocorrTest.EacNormal
31: [ OK ] AutocorrTest.EacNormal (24 ms)
31: [ RUN ] AutocorrTest.EacNoNormalize
31: [ OK ] AutocorrTest.EacNoNormalize (15 ms)
31: [ RUN ] AutocorrTest.EacCos
31: [ OK ] AutocorrTest.EacCos (25 ms)
31: [ RUN ] AutocorrTest.EacVector
31: [ OK ] AutocorrTest.EacVector (31 ms)
31: [ RUN ] AutocorrTest.EacRcross
31: [ OK ] AutocorrTest.EacRcross (6 ms)
31: [ RUN ] AutocorrTest.EacP0
31: [ OK ] AutocorrTest.EacP0 (31 ms)
31: [ RUN ] AutocorrTest.EacP1
31: [ OK ] AutocorrTest.EacP1 (31 ms)
31: [ RUN ] AutocorrTest.EacP2
31: [ OK ] AutocorrTest.EacP2 (59 ms)
31: [ RUN ] AutocorrTest.EacP3
31: [ OK ] AutocorrTest.EacP3 (15 ms)
31: [ RUN ] AutocorrTest.EacP4
31: [ OK ] AutocorrTest.EacP4 (31 ms)
31: [----------] 10 tests from AutocorrTest (280 ms total)
31:
31: [----------] 1 test from ManyAutocorrelationTest
31: [ RUN ] ManyAutocorrelationTest.Empty
31: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
31: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 11 tests from 2 test cases ran. (299 ms total)
31: [ PASSED ] 11 tests.
31/40 Test #31: CorrelationsTest ................. Passed 0.34 sec
test 32
Start 32: AnalysisDataUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 69 tests from 14 test cases.
32: [----------] Global test environment set-up.
32: [----------] 3 tests from AnalysisDataInitializationTest
32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
32: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/0 (13 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms)
32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/1 (16 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/2 (23 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/3 (26 ms total)
32:
32: [----------] 4 tests from AnalysisArrayDataTest
32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
32: [ RUN ] AnalysisArrayDataTest.StorageWorks
32: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms)
32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
32: [----------] 4 tests from AnalysisArrayDataTest (5 ms total)
32:
32: [----------] 6 tests from AverageModuleTest
32: [ RUN ] AverageModuleTest.BasicTest
32: [ OK ] AverageModuleTest.BasicTest (24 ms)
32: [ RUN ] AverageModuleTest.HandlesMultipointData
32: [ OK ] AverageModuleTest.HandlesMultipointData (5 ms)
32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (6 ms)
32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (12 ms)
32: [ RUN ] AverageModuleTest.CanCustomizeXAxis
32: [ OK ] AverageModuleTest.CanCustomizeXAxis (5 ms)
32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
32: [----------] 6 tests from AverageModuleTest (57 ms total)
32:
32: [----------] 2 tests from FrameAverageModuleTest
32: [ RUN ] FrameAverageModuleTest.BasicTest
32: [ OK ] FrameAverageModuleTest.BasicTest (3 ms)
32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (4 ms)
32: [----------] 2 tests from FrameAverageModuleTest (8 ms total)
32:
32: [----------] 7 tests from AnalysisHistogramSettingsTest
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
32: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
32:
32: [----------] 2 tests from SimpleHistogramModuleTest
32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (5 ms)
32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (5 ms)
32: [----------] 2 tests from SimpleHistogramModuleTest (11 ms total)
32:
32: [----------] 3 tests from WeightedHistogramModuleTest
32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (5 ms)
32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (5 ms)
32: [----------] 3 tests from WeightedHistogramModuleTest (17 ms total)
32:
32: [----------] 3 tests from BinAverageModuleTest
32: [ RUN ] BinAverageModuleTest.ComputesCorrectly
32: [ OK ] BinAverageModuleTest.ComputesCorrectly (4 ms)
32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (4 ms)
32: [----------] 3 tests from BinAverageModuleTest (13 ms total)
32:
32: [----------] 4 tests from AbstractAverageHistogramTest
32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (5 ms)
32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (5 ms)
32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (5 ms)
32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (5 ms)
32: [----------] 4 tests from AbstractAverageHistogramTest (20 ms total)
32:
32: [----------] 3 tests from LifetimeModuleTest
32: [ RUN ] LifetimeModuleTest.BasicTest
32: [ OK ] LifetimeModuleTest.BasicTest (3 ms)
32: [ RUN ] LifetimeModuleTest.CumulativeTest
32: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (3 ms)
32: [----------] 3 tests from LifetimeModuleTest (11 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 69 tests from 14 test cases ran. (224 ms total)
32: [ PASSED ] 69 tests.
32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.27 sec
test 33
Start 33: SelectionUnitTests
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 190 tests from 10 test cases.
33: [----------] Global test environment set-up.
33: [----------] 1 test from IndexGroupTest
33: [ RUN ] IndexGroupTest.RemovesDuplicates
33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
33: [----------] 1 test from IndexGroupTest (1 ms total)
33:
33: [----------] 15 tests from IndexBlockTest
33: [ RUN ] IndexBlockTest.CreatesUnknownBlock
33: [ OK ] IndexBlockTest.CreatesUnknownBlock (10 ms)
33: [ RUN ] IndexBlockTest.CreatesAtomBlock
33: [ OK ] IndexBlockTest.CreatesAtomBlock (2 ms)
33: [ RUN ] IndexBlockTest.CreatesResidueBlock
33: [ OK ] IndexBlockTest.CreatesResidueBlock (9 ms)
33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock
33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion
33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (1 ms)
33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion
33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (0 ms)
33: [ RUN ] IndexBlockTest.CreatesSingleBlock
33: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (2 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (1 ms)
33: [----------] 15 tests from IndexBlockTest (26 ms total)
33:
33: [----------] 11 tests from IndexMapTest
33: [ RUN ] IndexMapTest.InitializesAtomBlock
33: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (2 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms)
33: [ RUN ] IndexMapTest.InitializesMoleculeBlock
33: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
33: [ RUN ] IndexMapTest.MapsSingleBlock
33: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
33: [ RUN ] IndexMapTest.MapsResidueBlocks
33: [ OK ] IndexMapTest.MapsResidueBlocks (13 ms)
33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms)
33: [ RUN ] IndexMapTest.HandlesMultipleRequests
33: [ OK ] IndexMapTest.HandlesMultipleRequests (3 ms)
33: [----------] 11 tests from IndexMapTest (24 ms total)
33:
33: [----------] 15 tests from NeighborhoodSearchTest
33: [ RUN ] NeighborhoodSearchTest.SimpleSearch
33: [ OK ] NeighborhoodSearchTest.SimpleSearch (65 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (69 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchBox
33: [ OK ] NeighborhoodSearchTest.GridSearchBox (10 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (60 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (23 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (10 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (12 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (184 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (15 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
33: [----------] 15 tests from NeighborhoodSearchTest (453 ms total)
33:
33: [----------] 12 tests from PositionCalculationTest
33: [ RUN ] PositionCalculationTest.ComputesAtomPositions
33: [ OK ] PositionCalculationTest.ComputesAtomPositions (12 ms)
33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (64 ms)
33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (2 ms)
33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (2 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (2 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionMask
33: [ OK ] PositionCalculationTest.ComputesPositionMask (2 ms)
33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (2 ms)
33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (2 ms)
33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (2 ms)
33: [----------] 12 tests from PositionCalculationTest (96 ms total)
33:
33: [----------] 30 tests from SelectionCollectionTest
33: [ RUN ] SelectionCollectionTest.HandlesNoSelections
33: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions
33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
33: [----------] 30 tests from SelectionCollectionTest (47 ms total)
33:
33: [----------] 14 tests from SelectionCollectionInteractiveTest
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (3 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
33: [----------] 14 tests from SelectionCollectionInteractiveTest (32 ms total)
33:
33: [----------] 66 tests from SelectionCollectionDataTest
33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResnr
33: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesChain
33: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMass
33: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesCharge
33: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBeta
33: [ OK ] SelectionCollectionDataTest.HandlesBeta (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResname
33: [ OK ] SelectionCollectionDataTest.HandlesResname (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (7 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (23 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (8 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (8 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (9 ms)
33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (7 ms)
33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (7 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
33: [----------] 66 tests from SelectionCollectionDataTest (278 ms total)
33:
33: [----------] 17 tests from SelectionOptionTest
33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
33: [ RUN ] SelectionOptionTest.ChecksEmptySelections
33: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (2 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooManySelections
33: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesAdjuster
33: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
33: [----------] 17 tests from SelectionOptionTest (20 ms total)
33:
33: [----------] 9 tests from SelectionFileOptionTest
33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
33: [----------] 9 tests from SelectionFileOptionTest (12 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 190 tests from 10 test cases ran. (989 ms total)
33: [ PASSED ] 190 tests.
33/40 Test #33: SelectionUnitTests ............... Passed 1.05 sec
test 34
Start 34: TrajectoryAnalysisUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 74 tests from 14 test cases.
34: [----------] Global test environment set-up.
34: [----------] 5 tests from ClustsizeTest
34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
34: There is one group in the index
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 24
34: cmid: 2, cmax: 4, max_size: 6
34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (18 ms)
34: [ RUN ] ClustsizeTest.NoMolShortCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
34: There is one group in the index
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 24
34: cmid: 1, cmax: 6, max_size: 6
34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (8 ms)
34: [ RUN ] ClustsizeTest.MolDefaultCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 2, cmax: 4, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (12 ms)
34: [ RUN ] ClustsizeTest.MolShortCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 1, cmax: 6, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (10 ms)
34: [ RUN ] ClustsizeTest.MolCSize
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 2, cmax: 4, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolCSize (10 ms)
34: [----------] 5 tests from ClustsizeTest (60 ms total)
34:
34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (8 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
34: Reading frames from gro file 'Test system', 8 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (13 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
34: Reading frames from gro file 'Test system', 8 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (12 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (36 ms total)
34:
34: [----------] 11 tests from AngleModuleTest
34: [ RUN ] AngleModuleTest.ComputesSimpleAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesSimpleAngles (26 ms)
34: [ RUN ] AngleModuleTest.ComputesDihedrals
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesDihedrals (14 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (25 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (14 ms)
34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (14 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (19 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
34: Reading frames from gro file 'Test system for different angles', 33 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (17 ms)
34: [ RUN ] AngleModuleTest.ComputesMultipleAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
34: [ RUN ] AngleModuleTest.HandlesDynamicSelections
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesDynamicSelections (14 ms)
34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (14 ms)
34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (15 ms)
34: [----------] 11 tests from AngleModuleTest (190 ms total)
34:
34: [----------] 3 tests from DistanceModuleTest
34: [ RUN ] DistanceModuleTest.ComputesDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2:
34: Number of samples: 5
34: Average distance: 1.43246 nm
34: Standard deviation: 0.96700 nm
34: [ OK ] DistanceModuleTest.ComputesDistances (17 ms)
34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2:
34: Number of samples: 5
34: Average distance: 1.43246 nm
34: Standard deviation: 0.96700 nm
34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
34: Number of samples: 4
34: Average distance: 1.81066 nm
34: Standard deviation: 0.79289 nm
34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (22 ms)
34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2 and res_cog x < 2.8:
34: Number of samples: 3
34: Average distance: 1.72076 nm
34: Standard deviation: 1.24839 nm
34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (31 ms)
34: [----------] 3 tests from DistanceModuleTest (72 ms total)
34:
34: [----------] 2 tests from FreeVolumeModuleTest
34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for 40 particles. These were set to zero.
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: cutoff = 0.18 nm
34: probe_radius = 0 nm
34: seed = 13
34: ninsert = 1000 probes per nm^3
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
34: van der Spoel and Luciano T. Costa
34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
34: -------- -------- --- Thank You --- -------- --------
34:
34: Free volume 38.02 +/- 0.00 %
34: Total volume 68.92 +/- 0.00 nm^3
34: Number of molecules 340 total mass 63491.38 Dalton
34: Average molar mass: 186.74 Dalton
34: Density rho: 1529.71 +/- 0.00 nm^3
34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
34: Fractional free volume 0.194 +/- 0.000
34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (498 ms)
34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: cutoff = 0.18 nm
34: probe_radius = 0 nm
34: seed = 17
34: ninsert = 1000 probes per nm^3
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
34: van der Spoel and Luciano T. Costa
34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
34: -------- -------- --- Thank You --- -------- --------
34:
34: Free volume 38.48 +/- 0.00 %
34: Total volume 68.92 +/- 0.00 nm^3
34: Number of molecules 340 total mass 63491.38 Dalton
34: Average molar mass: 186.74 Dalton
34: Density rho: 1529.71 +/- 0.00 nm^3
34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
34: Fractional free volume 0.200 +/- 0.000
34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (537 ms)
34: [----------] 2 tests from FreeVolumeModuleTest (1036 ms total)
34:
34: [----------] 7 tests from PairDistanceModuleTest
34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (17 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (18 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (16 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (17 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (17 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (17 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (17 ms)
34: [----------] 7 tests from PairDistanceModuleTest (121 ms total)
34:
34: [----------] 5 tests from RdfModuleTest
34: [ RUN ] RdfModuleTest.BasicTest
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.BasicTest (186 ms)
34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (82 ms)
34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (116 ms)
34: [ RUN ] RdfModuleTest.CalculatesSurf
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.CalculatesSurf (61 ms)
34: [ RUN ] RdfModuleTest.CalculatesXY
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.CalculatesXY (108 ms)
34: [----------] 5 tests from RdfModuleTest (554 ms total)
34:
34: [----------] 5 tests from SasaModuleTest
34: [ RUN ] SasaModuleTest.BasicTest
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.BasicTest (45 ms)
34: [ RUN ] SasaModuleTest.HandlesSelectedResidues
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesSelectedResidues (37 ms)
34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (40 ms)
34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (46 ms)
34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (38 ms)
34: [----------] 5 tests from SasaModuleTest (214 ms total)
34:
34: [----------] 8 tests from SelectModuleTest
34: [ RUN ] SelectModuleTest.BasicTest
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.BasicTest (30 ms)
34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (21 ms)
34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (21 ms)
34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (21 ms)
34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (21 ms)
34: [ RUN ] SelectModuleTest.NormalizesSizes
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.NormalizesSizes (14 ms)
34: [ RUN ] SelectModuleTest.WritesResidueNumbers
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.WritesResidueNumbers (13 ms)
34: [ RUN ] SelectModuleTest.WritesResidueIndices
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.WritesResidueIndices (12 ms)
34: [----------] 8 tests from SelectModuleTest (155 ms total)
34:
34: [----------] 10 tests from SurfaceAreaTest
34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (3 ms)
34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (3 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints12
34: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints32
34: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints42
34: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints122
34: [ OK ] SurfaceAreaTest.SurfacePoints122 (3 ms)
34: [ RUN ] SurfaceAreaTest.Computes100Points
34: [ OK ] SurfaceAreaTest.Computes100Points (2 ms)
34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (9 ms)
34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (11 ms)
34: [----------] 10 tests from SurfaceAreaTest (37 ms total)
34:
34: [----------] 4 tests from TopologyInformation
34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
34: [ RUN ] TopologyInformation.WorksWithGroFile
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TopologyInformation.WorksWithGroFile (12 ms)
34: [ RUN ] TopologyInformation.WorksWithPdbFile
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TopologyInformation.WorksWithPdbFile (11 ms)
34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
34:
34: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]:
34: /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
34: scheme was introduced, but the group scheme was still the default. The
34: default is now the Verlet scheme, so you will observe different behaviour.
34:
34:
34: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: For a correct single-point energy evaluation with nsteps = 0, use
34: continuation = yes to avoid constraining the input coordinates.
34:
34: Setting the LD random seed to -57473001
34: Generated 330891 of the 330891 non-bonded parameter combinations
34: Generating 1-4 interactions: fudge = 0.5
34: Generated 330891 of the 330891 1-4 parameter combinations
34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
34:
34: NOTE 3 [file lysozyme.top, line 1465]:
34: System has non-zero total charge: 2.000000
34: Total charge should normally be an integer. See
34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
34: for discussion on how close it should be to an integer.
34:
34:
34:
34: Removing all charge groups because cutoff-scheme=Verlet
34: Number of degrees of freedom in T-Coupling group rest is 465.00
34:
34: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: NVE simulation with an initial temperature of zero: will use a Verlet
34: buffer of 10%. Check your energy drift!
34:
34:
34: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: You are using a plain Coulomb cut-off, which might produce artifacts.
34: You might want to consider using PME electrostatics.
34:
34:
34:
34: There were 5 notes
34: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.3 (single precision)
34: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.3 (single precision)
34: Analysing residue names:
34: There are: 10 Protein residues
34: Analysing Protein...
34: This run will generate roughly 0 Mb of data
34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1231 ms)
34: [----------] 4 tests from TopologyInformation (1257 ms total)
34:
34: [----------] 4 tests from TrajectoryModuleTest
34: [ RUN ] TrajectoryModuleTest.BasicTest
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.BasicTest (28 ms)
34: [ RUN ] TrajectoryModuleTest.PlotsXOnly
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.PlotsXOnly (25 ms)
34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (23 ms)
34: [ RUN ] TrajectoryModuleTest.HandlesNoForces
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.HandlesNoForces (23 ms)
34: [----------] 4 tests from TrajectoryModuleTest (105 ms total)
34:
34: [----------] 5 tests from UnionFinderTest
34: [ RUN ] UnionFinderTest.WorksEmpty
34: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
34: [ RUN ] UnionFinderTest.BasicMerges
34: [ OK ] UnionFinderTest.BasicMerges (0 ms)
34: [ RUN ] UnionFinderTest.LargerMerges
34: [ OK ] UnionFinderTest.LargerMerges (0 ms)
34: [ RUN ] UnionFinderTest.LongRightMerge
34: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
34: [ RUN ] UnionFinderTest.LongLeftMerge
34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
34: [----------] 5 tests from UnionFinderTest (1 ms total)
34:
34: [----------] 1 test from MappedUnionFinderTest
34: [ RUN ] MappedUnionFinderTest.BasicMerges
34: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
34: [----------] 1 test from MappedUnionFinderTest (0 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 74 tests from 14 test cases ran. (3840 ms total)
34: [ PASSED ] 74 tests.
34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 3.90 sec
test 35
Start 35: EnergyAnalysisUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 7 tests from 4 test cases.
35: [----------] Global test environment set-up.
35: [----------] 1 test from DhdlTest
35: [ RUN ] DhdlTest.ExtractDhdl
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
35: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
35: Note: file tpx version 110, software tpx version 116
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
35:
35:
35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
35: [ OK ] DhdlTest.ExtractDhdl (41 ms)
35: [----------] 1 test from DhdlTest (43 ms total)
35:
35: [----------] 1 test from OriresTest
35: [ RUN ] OriresTest.ExtractOrires
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
35: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
35: Note: file tpx version 111, software tpx version 116
35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
35: End your selection with 0
35: Selecting all 7 orientation restraints
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
35: [ OK ] OriresTest.ExtractOrires (72 ms)
35: [----------] 1 test from OriresTest (73 ms total)
35:
35: [----------] 3 tests from EnergyTest
35: [ RUN ] EnergyTest.ExtractEnergy
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
35: [ OK ] EnergyTest.ExtractEnergy (15 ms)
35: [ RUN ] EnergyTest.ExtractEnergyByNumber
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
35: Pres. DC -268.49 3 8.52175 13.2804 (bar)
35: [ OK ] EnergyTest.ExtractEnergyByNumber (12 ms)
35: [ RUN ] EnergyTest.ExtractEnergyMixed
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: [ OK ] EnergyTest.ExtractEnergyMixed (13 ms)
35: [----------] 3 tests from EnergyTest (43 ms total)
35:
35: [----------] 2 tests from ViscosityTest
35: [ RUN ] ViscosityTest.EinsteinViscosity
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Pres-XX 20.2092 65 717.193 185.978 (bar)
35: Pres-XY -47.7351 39 372.522 207.456 (bar)
35: Pres-XZ 11.477 31 379.79 6.80818 (bar)
35: Pres-YX -47.7106 39 372.525 207.5 (bar)
35: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
35: Pres-YZ -41.3534 45 401.216 114.663 (bar)
35: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
35: Pres-ZY -41.3119 45 401.196 114.743 (bar)
35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
35: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: [ OK ] ViscosityTest.EinsteinViscosity (45 ms)
35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Pres-XX 20.2092 65 717.193 185.978 (bar)
35: Pres-XY -47.7351 39 372.522 207.456 (bar)
35: Pres-XZ 11.477 31 379.79 6.80818 (bar)
35: Pres-YX -47.7106 39 372.525 207.5 (bar)
35: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
35: Pres-YZ -41.3534 45 401.216 114.663 (bar)
35: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
35: Pres-ZY -41.3119 45 401.196 114.743 (bar)
35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
35: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (40 ms)
35: [----------] 2 tests from ViscosityTest (86 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 7 tests from 4 test cases ran. (245 ms total)
35: [ PASSED ] 7 tests.
35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.29 sec
test 36
Start 36: ToolUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 4 tests from 1 test case.
36: [----------] Global test environment set-up.
36: [----------] 4 tests from ReportMethodsTest
36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (1 ms)
36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
36: [ RUN ] ReportMethodsTest.WritesCorrectInformation
36:
36: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]:
36: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
36: scheme was introduced, but the group scheme was still the default. The
36: default is now the Verlet scheme, so you will observe different behaviour.
36:
36:
36: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: For a correct single-point energy evaluation with nsteps = 0, use
36: continuation = yes to avoid constraining the input coordinates.
36:
36: Setting the LD random seed to 1206391681
36: Generated 330891 of the 330891 non-bonded parameter combinations
36: Generating 1-4 interactions: fudge = 0.5
36: Generated 330891 of the 330891 1-4 parameter combinations
36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
36:
36: NOTE 3 [file lysozyme.top, line 1465]:
36: System has non-zero total charge: 2.000000
36: Total charge should normally be an integer. See
36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
36: for discussion on how close it should be to an integer.
36:
36:
36:
36: Removing all charge groups because cutoff-scheme=Verlet
36: Number of degrees of freedom in T-Coupling group rest is 465.00
36:
36: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: NVE simulation with an initial temperature of zero: will use a Verlet
36: buffer of 10%. Check your energy drift!
36:
36:
36: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: You are using a plain Coulomb cut-off, which might produce artifacts.
36: You might want to consider using PME electrostatics.
36:
36:
36:
36: There were 5 notes
36: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.3 (single precision)
36: Analysing residue names:
36: There are: 10 Protein residues
36: Analysing Protein...
36: This run will generate roughly 0 Mb of data
36: [ OK ] ReportMethodsTest.WritesCorrectInformation (1253 ms)
36: [ RUN ] ReportMethodsTest.ToolEndToEndTest
36:
36: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]:
36: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
36: scheme was introduced, but the group scheme was still the default. The
36: default is now the Verlet scheme, so you will observe different behaviour.
36:
36:
36: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: For a correct single-point energy evaluation with nsteps = 0, use
36: continuation = yes to avoid constraining the input coordinates.
36:
36: Setting the LD random seed to -841899246
36: Generated 330891 of the 330891 non-bonded parameter combinations
36: Generating 1-4 interactions: fudge = 0.5
36: Generated 330891 of the 330891 1-4 parameter combinations
36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
36:
36: NOTE 3 [file lysozyme.top, line 1465]:
36: System has non-zero total charge: 2.000000
36: Total charge should normally be an integer. See
36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
36: for discussion on how close it should be to an integer.
36:
36:
36:
36: Removing all charge groups because cutoff-scheme=Verlet
36: Number of degrees of freedom in T-Coupling group rest is 465.00
36:
36: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: NVE simulation with an initial temperature of zero: will use a Verlet
36: buffer of 10%. Check your energy drift!
36:
36:
36: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: You are using a plain Coulomb cut-off, which might produce artifacts.
36: You might want to consider using PME electrostatics.
36:
36:
36:
36: There were 5 notes
36: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.3 (single precision)
36: Analysing residue names:
36: There are: 10 Protein residues
36: Analysing Protein...
36: This run will generate roughly 0 Mb of data
36: section: Methods
36: subsection: Simulation system
36: A system of 1 molecules (156 atoms) was simulated.
36:
36: subsection: Simulation settings
36: A total of 0 ns were simulated with a time step of 1 fs.
36: Neighbor searching was performed every 10 steps.
36: The Cut-off algorithm was used for electrostatic interactions.
36: with a cut-off of 1 nm.
36: A single cut-off of 1.1 nm was used for Van der Waals interactions.
36: [ OK ] ReportMethodsTest.ToolEndToEndTest (1276 ms)
36: [----------] 4 tests from ReportMethodsTest (2530 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 4 tests from 1 test case ran. (2530 ms total)
36: [ PASSED ] 4 tests.
36/40 Test #36: ToolUnitTests .................... Passed 2.58 sec
test 37
Start 37: MdrunTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
37: Test timeout computed to be: 600
37: [==========] Running 29 tests from 11 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from GromppTest
37: [ RUN ] GromppTest.EmptyMdpFileWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 456511783
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 12.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: NVE simulation: will use the initial temperature of 1046.791 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37: [ OK ] GromppTest.EmptyMdpFileWorks (186 ms)
37: [----------] 1 test from GromppTest (186 ms total)
37:
37: [----------] 1 test from ImdTest
37: [ RUN ] ImdTest.ImdCanRun
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]:
37: The Berendsen thermostat does not generate the correct kinetic energy
37: distribution. You might want to consider using the V-rescale thermostat.
37:
37: Setting the LD random seed to -1009289168
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD).
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 50, rlist from 1.121 to 1.344
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: IMD: Enabled. This simulation will accept incoming IMD connections.
37: IMD: You chose a port number < 1. Will automatically assign a free port.
37: IMD: Pulling from IMD remote is enabled (-imdpull).
37: IMD: Turning on IMD - port for incoming requests is 0.
37: IMD: Setting up incoming socket.
37: IMD: Listening for IMD connection on port 33285.
37: IMD: -imdwait not set, starting simulation.
37: starting mdrun 'spc2'
37: 2 steps, 0.0 ps.
37: turning all bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.464 0.232 199.8
37: (ns/day) (hour/ns)
37: Performance: 4.462 5.379
37: [ OK ] ImdTest.ImdCanRun (283 ms)
37: [----------] 1 test from ImdTest (283 ms total)
37:
37: [----------] 2 tests from PmeTest
37: [ RUN ] PmeTest.ReproducesEnergies
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -424512683
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
37: NVE simulation: will use the initial temperature of 1046.791 K for
37: determining the Verlet buffer size
37:
37: Estimate for the relative computational load of the PME mesh part: 1.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
37: The optimal PME mesh load for parallel simulations is below 0.5
37: and for highly parallel simulations between 0.25 and 0.33,
37: for higher performance, increase the cut-off and the PME grid spacing.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: Calculating fourier grid dimensions for X Y Z
37: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.511 0.256 199.9
37: (ns/day) (hour/ns)
37: Performance: 7.094 3.383
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.437 0.219 199.8
37: (ns/day) (hour/ns)
37: Performance: 8.302 2.891
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37:
37: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.466 0.233 199.9
37: (ns/day) (hour/ns)
37: Performance: 7.776 3.086
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10927 ms)
37: [ RUN ] PmeTest.ScalesTheBox
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 609908976
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Searching the wall atom type(s)
37: Number of degrees of freedom in T-Coupling group rest is 13.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: NVE simulation: will use the initial temperature of 966.268 K for
37: determining the Verlet buffer size
37:
37: Estimate for the relative computational load of the PME mesh part: 1.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: The optimal PME mesh load for parallel simulations is below 0.5
37: and for highly parallel simulations between 0.25 and 0.33,
37: for higher performance, increase the cut-off and the PME grid spacing.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 0 steps, 0.0 ps.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.034 0.017 195.4
37: (ns/day) (hour/ns)
37: Performance: 4.983 4.816
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: Calculating fourier grid dimensions for X Y Z
37: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
37: This run will generate roughly 0 Mb of data
37: [ OK ] PmeTest.ScalesTheBox (31130 ms)
37: [----------] 2 tests from PmeTest (42057 ms total)
37:
37: [----------] 1 test from CompelTest
37: [ RUN ] CompelTest.SwapCanRun
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
37: The Berendsen thermostat does not generate the correct kinetic energy
37: distribution. You might want to consider using the V-rescale thermostat.
37:
37: Setting the LD random seed to -1825291693
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein'
37: Excluding 3 bonded neighbours molecule type 'OCT'
37: Excluding 1 bonded neighbours molecule type 'NA'
37: Excluding 1 bonded neighbours molecule type 'CL'
37: Excluding 3 bonded neighbours molecule type 'Protein'
37: Excluding 3 bonded neighbours molecule type 'OCT'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Split0 group 'Ch0' contains 83 atoms.
37: Split1 group 'Ch1' contains 83 atoms.
37: Solvent group 'SOL' contains 11931 atoms.
37: Swap group 'NA+' contains 19 atoms.
37: Swap group 'CL-' contains 19 atoms.
37: Number of degrees of freedom in T-Coupling group System is 27869.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.3 (single precision)
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: SWAP: Determining initial numbers of ions per compartment.
37: SWAP: Setting pointers for checkpoint writing
37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
37: starting mdrun 'Channel_coco in octane membrane'
37: 2 steps, 0.0 ps.
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 1 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 4.307 2.154 200.0
37: (ns/day) (hour/ns)
37: Performance: 0.602 39.881
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.3 (single precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: SWAP: Setting pointers for checkpoint writing
37: SWAP: Copying channel fluxes from checkpoint file data
37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
37: starting mdrun 'Channel_coco in octane membrane'
37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 3.779 1.890 200.0
37: (ns/day) (hour/ns)
37: Performance: 0.686 34.999
37: [ OK ] CompelTest.SwapCanRun (6474 ms)
37: [----------] 1 test from CompelTest (6474 ms total)
37:
37: [----------] 6 tests from BondedInteractionsTest
37: [ RUN ] BondedInteractionsTest.NormalBondWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1213453276
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 2 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.002 0.001 188.5
37: (ns/day) (hour/ns)
37: Performance: 69.663 0.345
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalBondWorks (30 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1013332729
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 2 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 191.7
37: (ns/day) (hour/ns)
37: Performance: 42.770 0.561
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (39 ms)
37: [ RUN ] BondedInteractionsTest.NormalAngleWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 458568634
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 1 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 192.1
37: (ns/day) (hour/ns)
37: Performance: 44.318 0.542
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalAngleWorks (36 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1861692421
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 1 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 191.7
37: (ns/day) (hour/ns)
37: Performance: 44.492 0.539
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (51 ms)
37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -721737609
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 191.8
37: (ns/day) (hour/ns)
37: Performance: 44.454 0.540
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (36 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -808375301
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 191.8
37: (ns/day) (hour/ns)
37: Performance: 44.140 0.544
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (53 ms)
37: [----------] 6 tests from BondedInteractionsTest (247 ms total)
37:
37: [----------] 2 tests from MdrunTerminationTest
37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -1252909635
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 1, rlist from 1.024 to 1
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 100 steps, 0.1 ps.
37:
37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.315 0.158 199.8
37: (ns/day) (hour/ns)
37: Performance: 1.097 21.881
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.3 (single precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps
37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
37:
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps).
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.313 0.157 199.8
37: (ns/day) (hour/ns)
37: Performance: 1.652 14.527
37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (365 ms)
37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 905247577
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 1, rlist from 1.024 to 1
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 100 steps, 0.1 ps.
37:
37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.308 0.154 199.8
37: (ns/day) (hour/ns)
37: Performance: 1.121 21.405
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.3 (single precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps
37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
37:
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps).
37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.311 0.156 199.9
37: (ns/day) (hour/ns)
37: Performance: 1.665 14.418
37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (349 ms)
37: [----------] 2 tests from MdrunTerminationTest (715 ms total)
37:
37: [----------] 4 tests from MimicTest
37: [ RUN ] MimicTest.OneQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1056227604
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 193.3
37: (ns/day) (hour/ns)
37: Performance: 41.444 0.579
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.OneQuantumMol (31 ms)
37: [ RUN ] MimicTest.AllQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 287516999
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.005 0.003 193.6
37: (ns/day) (hour/ns)
37: Performance: 34.085 0.704
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.AllQuantumMol (33 ms)
37: [ RUN ] MimicTest.TwoQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 993431746
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.005 0.003 194.4
37: (ns/day) (hour/ns)
37: Performance: 34.268 0.700
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.TwoQuantumMol (35 ms)
37: [ RUN ] MimicTest.BondCuts
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 953676373
37: Generated 2211 of the 2211 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 2211 of the 2211 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 66.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: NVE simulation: will use the initial temperature of 300.368 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/ala.gro'
37:
37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.005 0.003 194.7
37: (ns/day) (hour/ns)
37: Performance: 31.259 0.768
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.BondCuts (98 ms)
37: [----------] 4 tests from MimicTest (198 ms total)
37:
37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
37: Setting the LD random seed to -981656466
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.360 0.180 199.8
37: (ns/day) (hour/ns)
37: Performance: 0.958 25.048
37:
Reading frame 0 time 0.000
37: # Atoms 6
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (211 ms)
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
37: Setting the LD random seed to -49666929
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.314 0.157 199.8
37: (ns/day) (hour/ns)
37: Performance: 1.100 21.824
37:
Reading frame 0 time 0.000
37: # Atoms 6
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (182 ms)
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
37: Setting the LD random seed to 1228729646
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.365 0.183 199.8
37: (ns/day) (hour/ns)
37: Performance: 0.945 25.387
37:
Reading frame 0 time 0.000
37: # Atoms 3
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (209 ms)
37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (602 ms total)
37:
37: [----------] 3 tests from Checking/InitialConstraintsTest
37: [ RUN ] Checking/InitialConstraintsTest.Works/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 391062199
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.266 0.133 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.296 18.518
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (263 ms)
37: [ RUN ] Checking/InitialConstraintsTest.Works/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -741597160
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.304 0.152 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.134 21.166
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (274 ms)
37: [ RUN ] Checking/InitialConstraintsTest.Works/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: Integrator method md-vv-avek is implemented primarily for validation
37: purposes; for molecular dynamics, you should probably be using md or md-vv
37:
37: Setting the LD random seed to 843314796
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.3 (single precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.277 0.139 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.245 19.279
37: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (266 ms)
37: [----------] 3 tests from Checking/InitialConstraintsTest (803 ms total)
37:
37: [----------] 3 tests from MdrunCanWrite/Trajectories
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1186295774
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.295 0.148 199.7
37: (ns/day) (hour/ns)
37: Performance: 4.092 5.865
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (267 ms)
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1009840944
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.352 0.176 199.8
37: (ns/day) (hour/ns)
37: Performance: 3.429 6.998
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (282 ms)
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 347175764
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.331 0.166 199.8
37: (ns/day) (hour/ns)
37: Performance: 3.653 6.569
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (307 ms)
37: [----------] 3 tests from MdrunCanWrite/Trajectories (856 ms total)
37:
37: [----------] 3 tests from MdrunCanWrite/NptTrajectories
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -865965093
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.316 0.158 199.8
37: (ns/day) (hour/ns)
37: Performance: 1.638 14.651
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (283 ms)
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 225948399
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.307 0.154 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.684 14.248
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (283 ms)
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -751296173
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.3 (single precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.323 0.162 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.604 14.965
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (291 ms)
37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (857 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 29 tests from 11 test cases ran. (53280 ms total)
37: [ PASSED ] 29 tests.
37/40 Test #37: MdrunTests ....................... Passed 53.35 sec
test 38
Start 38: MdrunNonIntegratorTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
38: Test timeout computed to be: 600
38: [==========] Running 57 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -4.7990990e+01
38: Maximum force = 1.8629828e+02 on atom 13
38: Norm of force = 8.7721844e+01
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1077 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 3.02331e+02 on atom 3
38: F-Norm = 1.18024e+02
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -5.5862099e+01
38: Maximum force = 4.2728845e+02 on atom 13
38: Norm of force = 1.8453478e+02
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1041 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 22.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 3.1937714e+02
38: Maximum force = 9.9988643e+03 on atom 9
38: Norm of force = 4.6166996e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (609 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38:
38: NOTE 3 [file glycine_vacuo.top, line 12]:
38: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
38:
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 22.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 2.41575e+04 on atom 10
38: F-Norm = 1.18451e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 1.5174377e+02
38: Maximum force = 7.4208838e+03 on atom 9
38: Norm of force = 3.5693005e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (431 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 3 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -1.5698413e+02
38: Maximum force = 4.5704984e+02 on atom 17
38: Norm of force = 1.8327747e+02
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (169 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 3 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38:
38: NOTE 4 [file unknown]:
38: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 1.06801e+03 on atom 28
38: F-Norm = 4.26916e+02
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -1.6941180e+02
38: Maximum force = 2.1832491e+02 on atom 17
38: Norm of force = 7.9220732e+01
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (86 ms)
38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3413 ms total)
38:
38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents converged to Fmax < 10 in 1 steps
38: Potential Energy = -9.7425699e-01
38: Maximum force = 4.0132303e+00 on atom 1
38: Norm of force = 1.6383944e+00
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (48 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 4.01323e+00 on atom 1
38: F-Norm = 1.63839e+00
38:
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
38: Potential Energy = -9.9064207e-01
38: Maximum force = 2.5781622e+00 on atom 1
38: Norm of force = 1.0525302e+00
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (47 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38:
38: There was 1 warning
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Low-Memory BFGS Minimizer:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: Using 10 BFGS correction steps.
38:
38: F-max = 4.01323e+00 on atom 1
38: F-Norm = 1.63839e+00
38:
38:
38: writing lowest energy coordinates.
38:
38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
38: Potential Energy = -9.9064207e-01
38: Maximum force = 2.5781622e+00 on atom 1
38: Norm of force = 1.0525302e+00
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (49 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 3.1939697e+02
38: Maximum force = 9.9704248e+03 on atom 9
38: Norm of force = 4.6227540e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (458 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 2.41672e+04 on atom 10
38: F-Norm = 1.19357e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 1.5625757e+02
38: Maximum force = 7.5018242e+03 on atom 9
38: Norm of force = 3.6139019e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (506 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38:
38: There was 1 warning
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Low-Memory BFGS Minimizer:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: Using 10 BFGS correction steps.
38:
38: F-max = 2.41672e+04 on atom 10
38: F-Norm = 1.19357e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 5.6111725e+02
38: Maximum force = 1.2685491e+04 on atom 10
38: Norm of force = 6.0643622e+03
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (500 ms)
38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1608 ms total)
38:
38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: NVE simulation: will use the initial temperature of 68.810 K for
38: determining the Verlet buffer size
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.486 0.243 199.9
38: (ns/day) (hour/ns)
38: Performance: 6.037 3.975
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr'
38:
38: trr version: GMX_trn_file (single precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.1
38: (ns/day) (hour/ns)
38: Performance: 416.594 0.058
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (328 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: NVE simulation: will use the initial temperature of 68.810 K for
38: determining the Verlet buffer size
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.414 0.207 199.8
38: (ns/day) (hour/ns)
38: Performance: 7.094 3.383
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.6
38: (ns/day) (hour/ns)
38: Performance: 399.131 0.060
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (301 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.420 0.210 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.995 3.431
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 192.9
38: (ns/day) (hour/ns)
38: Performance: 412.770 0.058
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (300 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.614 0.307 199.9
38: (ns/day) (hour/ns)
38: Performance: 4.779 5.022
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.5
38: (ns/day) (hour/ns)
38: Performance: 411.804 0.058
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (405 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: NVE simulation: will use the initial temperature of 398.997 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.504 0.252 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.820 4.124
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.008 0.004 195.8
38: (ns/day) (hour/ns)
38: Performance: 382.646 0.063
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (1400 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: NVE simulation: will use the initial temperature of 398.997 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.489 0.245 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.005 3.997
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.006 0.003 195.0
38: (ns/day) (hour/ns)
38: Performance: 451.160 0.053
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (1385 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.514 0.257 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.716 4.199
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.5
38: (ns/day) (hour/ns)
38: Performance: 394.986 0.061
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (1422 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.539 0.270 199.9
38: (ns/day) (hour/ns)
38: Performance: 5.448 4.405
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.005 0.003 195.0
38: (ns/day) (hour/ns)
38: Performance: 535.378 0.045
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1410 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: NVE simulation: will use the initial temperature of 456.887 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 7 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 7 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.423 0.212 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.937 3.460
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.008 0.004 196.6
38: (ns/day) (hour/ns)
38: Performance: 340.082 0.071
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (344 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: NVE simulation: will use the initial temperature of 456.887 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 7 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 7 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.455 0.228 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.452 3.720
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 196.6
38: (ns/day) (hour/ns)
38: Performance: 323.884 0.074
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (343 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 6 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.442 0.221 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.642 3.614
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.006 196.9
38: (ns/day) (hour/ns)
38: Performance: 261.997 0.092
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (453 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 6 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.446 0.223 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.572 3.652
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 196.6
38: (ns/day) (hour/ns)
38: Performance: 321.937 0.075
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (397 ms)
38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (8492 ms total)
38:
38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.561 0.281 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.227 4.592
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.018 0.009 191.2
38: (ns/day) (hour/ns)
38: Performance: 158.574 0.151
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (481 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.502 0.251 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.845 4.106
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 190.5
38: (ns/day) (hour/ns)
38: Performance: 273.914 0.088
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (381 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.544 0.272 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.391 4.452
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.7
38: (ns/day) (hour/ns)
38: Performance: 221.828 0.108
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (407 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.502 0.251 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.848 4.104
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.7
38: (ns/day) (hour/ns)
38: Performance: 221.987 0.108
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (410 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.602 0.301 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.874 4.924
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 190.4
38: (ns/day) (hour/ns)
38: Performance: 230.371 0.104
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (446 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.470 0.235 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.237 3.848
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.4
38: (ns/day) (hour/ns)
38: Performance: 221.931 0.108
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (393 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.486 0.243 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.035 3.977
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 190.3
38: (ns/day) (hour/ns)
38: Performance: 226.910 0.106
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (409 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.620 0.311 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.729 5.075
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 189.9
38: (ns/day) (hour/ns)
38: Performance: 282.053 0.085
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (445 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.433 0.217 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.771 3.544
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.5
38: (ns/day) (hour/ns)
38: Performance: 218.298 0.110
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (350 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.660 0.330 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.445 5.400
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.3
38: (ns/day) (hour/ns)
38: Performance: 222.992 0.108
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (474 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.568 0.284 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.164 4.647
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.6
38: (ns/day) (hour/ns)
38: Performance: 219.230 0.109
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (432 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.503 0.252 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.830 4.117
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.006 190.2
38: (ns/day) (hour/ns)
38: Performance: 267.016 0.090
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (379 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.544 0.273 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.389 4.453
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 187.8
38: (ns/day) (hour/ns)
38: Performance: 296.682 0.081
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (405 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.487 0.244 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.022 3.985
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 189.7
38: (ns/day) (hour/ns)
38: Performance: 296.197 0.081
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (368 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.720 0.360 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.075 5.890
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.023 0.012 194.4
38: (ns/day) (hour/ns)
38: Performance: 126.182 0.190
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (508 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.968 0.484 199.9
38: (ns/day) (hour/ns)
38: Performance: 3.033 7.913
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.014 0.007 191.1
38: (ns/day) (hour/ns)
38: Performance: 203.845 0.118
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (634 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.462 0.231 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.352 3.778
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 179.1
38: (ns/day) (hour/ns)
38: Performance: 267.666 0.090
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (371 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.580 0.290 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.059 4.744
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.007 177.9
38: (ns/day) (hour/ns)
38: Performance: 219.020 0.110
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (421 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.502 0.251 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.843 4.107
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.007 180.0
38: (ns/day) (hour/ns)
38: Performance: 215.752 0.111
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (393 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.713 0.357 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.118 5.828
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.006 180.4
38: (ns/day) (hour/ns)
38: Performance: 254.202 0.094
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (499 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.528 0.264 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.554 4.321
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 179.1
38: (ns/day) (hour/ns)
38: Performance: 274.390 0.087
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (384 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.576 0.288 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.096 4.709
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.3 (single precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 190.2
38: (ns/day) (hour/ns)
38: Performance: 242.295 0.099
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (422 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.467 0.234 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.282 3.820
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 190.0
38: (ns/day) (hour/ns)
38: Performance: 294.006 0.082
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (417 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.619 0.310 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.744 5.059
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 189.4
38: (ns/day) (hour/ns)
38: Performance: 298.189 0.080
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (483 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.573 0.287 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.123 4.685
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 192.0
38: (ns/day) (hour/ns)
38: Performance: 210.252 0.114
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (455 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.424 0.212 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.917 3.470
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.014 0.007 190.7
38: (ns/day) (hour/ns)
38: Performance: 202.965 0.118
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (398 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.475 0.238 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.181 3.883
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.006 190.3
38: (ns/day) (hour/ns)
38: Performance: 261.197 0.092
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (421 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.641 0.321 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.578 5.242
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.4
38: (ns/day) (hour/ns)
38: Performance: 214.282 0.112
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (498 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.429 0.215 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.832 3.513
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.3
38: (ns/day) (hour/ns)
38: Performance: 221.851 0.108
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (413 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.485 0.243 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.051 3.966
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.014 0.007 191.3
38: (ns/day) (hour/ns)
38: Performance: 198.639 0.121
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (442 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.458 0.229 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.403 3.748
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 189.9
38: (ns/day) (hour/ns)
38: Performance: 273.561 0.088
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (402 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.493 0.247 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.952 4.032
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 190.6
38: (ns/day) (hour/ns)
38: Performance: 211.952 0.113
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (454 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.613 0.307 199.8
38: (ns/day) (hour/ns)
38: Performance: 4.790 5.010
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.3 (single precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 188.5
38: (ns/day) (hour/ns)
38: Performance: 216.480 0.111
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as single precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (489 ms)
38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (14294 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 57 tests from 4 test cases ran. (27807 ms total)
38: [ PASSED ] 57 tests.
38/40 Test #38: MdrunNonIntegratorTests .......... Passed 27.90 sec
test 39
Start 39: LegacyGroupSchemeMdrunTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/legacy-mdrun-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml"
39: Test timeout computed to be: 600
39: [==========] Running 2 tests from 1 test case.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from Simple/TpiTest
39: [ RUN ] Simple/TpiTest.ReproducesOutput/0
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]:
39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
39: removed in a future release when all interaction forms are supported for
39: the verlet scheme. The verlet scheme already scales better, and it is
39: compatible with GPUs and other accelerators.
39:
39: Generated 331705 of the 331705 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 331705 of the 331705 1-4 parameter combinations
39: Excluding 2 bonded neighbours molecule type 'SOL'
39: Excluding 3 bonded neighbours molecule type 'methane'
39: Number of degrees of freedom in T-Coupling group System is 1308.00
39:
39: There was 1 note
39: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.3 (single precision)
39: Using 1 MPI thread
39:
39:
39: NOTE: Thread affinity was not set.
39:
39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
39: removed in a future release when 'verlet' supports all interaction forms.
39:
39: Reading frames from gro file '216 water molecules', 648 atoms.
39:
Reading frame 0 time 0.000 mu 8.698e+02 <mu> 8.698e+02
39:
Last frame 0 time 0.000
39: Analysing residue names:
39: There are: 216 Water residues
39: There are: 1 Other residues
39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm
39: Largest charge group radii for Coulomb: 0.100, 0.100 nm
39: This run will generate roughly 0 Mb of data
39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1134 ms)
39: [ RUN ] Simple/TpiTest.ReproducesOutput/1
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]:
39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
39: removed in a future release when all interaction forms are supported for
39: the verlet scheme. The verlet scheme already scales better, and it is
39: compatible with GPUs and other accelerators.
39:
39: Generated 331705 of the 331705 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 331705 of the 331705 1-4 parameter combinations
39: Excluding 2 bonded neighbours molecule type 'SOL'
39: Excluding 3 bonded neighbours molecule type 'methane'
39: Number of degrees of freedom in T-Coupling group System is 1308.00
39:
39: There was 1 note
39: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.3 (single precision)
39: Using 1 MPI thread
39:
39:
39: NOTE: Thread affinity was not set.
39:
39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
39: removed in a future release when 'verlet' supports all interaction forms.
39:
39: Reading frames from gro file '216 water molecules', 648 atoms.
39:
Reading frame 0 time 0.000 mu 9.151e+01 <mu> 9.151e+01
39:
Last frame 0 time 0.000
39: Analysing residue names:
39: There are: 216 Water residues
39: There are: 1 Other residues
39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm
39: Largest charge group radii for Coulomb: 0.100, 0.100 nm
39: This run will generate roughly 0 Mb of data
39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (1146 ms)
39: [----------] 2 tests from Simple/TpiTest (2281 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 2 tests from 1 test case ran. (2282 ms total)
39: [ PASSED ] 2 tests.
39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 2.32 sec
test 40
Start 40: MdrunMpiTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
40: Test timeout computed to be: 600
40: [==========] Running 21 tests from 7 test cases.
40: [----------] Global test environment set-up.
40: [----------] 1 test from DomainDecompositionSpecialCasesTest
40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 550652614
40: Generated 3 of the 3 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 3 of the 3 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 9.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc2'
40: 0 steps, 0.0 ps.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.002 0.001 176.4
40: (ns/day) (hour/ns)
40: Performance: 73.462 0.327
40: This run will generate roughly 0 Mb of data
40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (44 ms)
40: [----------] 1 test from DomainDecompositionSpecialCasesTest (45 ms total)
40:
40: [----------] 4 tests from MimicTest
40: [ RUN ] MimicTest.OneQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 1592592681
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.004 0.002 193.6
40: (ns/day) (hour/ns)
40: Performance: 39.906 0.601
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.OneQuantumMol (47 ms)
40: [ RUN ] MimicTest.AllQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 88940505
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.004 0.002 193.4
40: (ns/day) (hour/ns)
40: Performance: 41.769 0.575
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.AllQuantumMol (52 ms)
40: [ RUN ] MimicTest.TwoQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -553046006
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.003 0.002 192.4
40: (ns/day) (hour/ns)
40: Performance: 48.793 0.492
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.TwoQuantumMol (47 ms)
40: [ RUN ] MimicTest.BondCuts
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 1496593353
40: Generated 2211 of the 2211 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2211 of the 2211 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 66.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: NVE simulation: will use the initial temperature of 300.368 K for
40: determining the Verlet buffer size
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/ala.gro'
40:
40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.005 0.003 194.5
40: (ns/day) (hour/ns)
40: Performance: 32.209 0.745
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.BondCuts (86 ms)
40: [----------] 4 tests from MimicTest (233 ms total)
40:
40: [----------] 1 test from MultiSimTerminationTest
40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (1 ms)
40: [----------] 1 test from MultiSimTerminationTest (1 ms total)
40:
40: [----------] 2 tests from PmeTest
40: [ RUN ] PmeTest.ReproducesEnergies
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40: Setting the LD random seed to 1347251927
40: Generated 279 of the 1225 non-bonded parameter combinations
40: Excluding 2 bonded neighbours molecule type 'Methanol'
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 12.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
40: NVE simulation: will use the initial temperature of 1046.791 K for
40: determining the Verlet buffer size
40:
40: Estimate for the relative computational load of the PME mesh part: 1.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
40: The optimal PME mesh load for parallel simulations is below 0.5
40: and for highly parallel simulations between 0.25 and 0.33,
40: for higher performance, increase the cut-off and the PME grid spacing.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: Calculating fourier grid dimensions for X Y Z
40: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
40: This run will generate roughly 0 Mb of data
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.616 0.308 199.9
40: (ns/day) (hour/ns)
40: Performance: 5.885 4.078
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.446 0.223 199.8
40: (ns/day) (hour/ns)
40: Performance: 8.133 2.951
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.433 0.217 199.8
40: (ns/day) (hour/ns)
40: Performance: 8.365 2.869
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (10914 ms)
40: [ RUN ] PmeTest.ScalesTheBox
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -1687206425
40: Generated 279 of the 1225 non-bonded parameter combinations
40: Excluding 2 bonded neighbours molecule type 'Methanol'
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Searching the wall atom type(s)
40: Number of degrees of freedom in T-Coupling group rest is 13.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: NVE simulation: will use the initial temperature of 966.268 K for
40: determining the Verlet buffer size
40:
40: Estimate for the relative computational load of the PME mesh part: 1.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: The optimal PME mesh load for parallel simulations is below 0.5
40: and for highly parallel simulations between 0.25 and 0.33,
40: for higher performance, increase the cut-off and the PME grid spacing.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.3 (single precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 0 steps, 0.0 ps.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.026 0.013 195.7
40: (ns/day) (hour/ns)
40: Performance: 6.625 3.623
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: Calculating fourier grid dimensions for X Y Z
40: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
40: This run will generate roughly 0 Mb of data
40: [ OK ] PmeTest.ScalesTheBox (31037 ms)
40: [----------] 2 tests from PmeTest (41952 ms total)
40:
40: [----------] 1 test from ReplicaExchangeTerminationTest
40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
40:
40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -4.7990990e+01
40: Maximum force = 1.8629828e+02 on atom 13
40: Norm of force = 8.7721844e+01
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1046 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 3.02331e+02 on atom 3
40: F-Norm = 1.18024e+02
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -5.5862099e+01
40: Maximum force = 4.2728845e+02 on atom 13
40: Norm of force = 1.8453478e+02
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1084 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 22.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 3.1937714e+02
40: Maximum force = 9.9988643e+03 on atom 9
40: Norm of force = 4.6166996e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (424 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40:
40: NOTE 3 [file glycine_vacuo.top, line 12]:
40: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
40:
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 22.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 2.41575e+04 on atom 10
40: F-Norm = 1.18451e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 1.5174377e+02
40: Maximum force = 7.4208838e+03 on atom 9
40: Norm of force = 3.5693005e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (438 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 2145 of the 2145 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2145 of the 2145 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
40:
40: NOTE 3 [file unknown]:
40: You are using constraints on all bonds, whereas the forcefield has been
40: parametrized only with constraints involving hydrogen atoms. We suggest
40: using constraints = h-bonds instead, this will also improve performance.
40:
40: Cleaning up constraints and constant bonded interactions with virtual sites
40: Removed 18 Angles with virtual sites, 21 left
40: Removed 10 Proper Dih.s with virtual sites, 44 left
40: Converted 15 Constraints with virtual sites to connections, 7 left
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 23.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -1.5698413e+02
40: Maximum force = 4.5704984e+02 on atom 17
40: Norm of force = 1.8327747e+02
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (67 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 2145 of the 2145 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2145 of the 2145 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
40:
40: NOTE 3 [file unknown]:
40: You are using constraints on all bonds, whereas the forcefield has been
40: parametrized only with constraints involving hydrogen atoms. We suggest
40: using constraints = h-bonds instead, this will also improve performance.
40:
40:
40: NOTE 4 [file unknown]:
40: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
40:
40: Cleaning up constraints and constant bonded interactions with virtual sites
40: Removed 18 Angles with virtual sites, 21 left
40: Removed 10 Proper Dih.s with virtual sites, 44 left
40: Converted 15 Constraints with virtual sites to connections, 7 left
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 23.00
40:
40: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 5 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 1.06801e+03 on atom 28
40: F-Norm = 4.26916e+02
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -1.6941180e+02
40: Maximum force = 2.1832491e+02 on atom 17
40: Norm of force = 7.9220732e+01
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (69 ms)
40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (3130 ms total)
40:
40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents converged to Fmax < 10 in 1 steps
40: Potential Energy = -9.7425699e-01
40: Maximum force = 4.0132303e+00 on atom 1
40: Norm of force = 1.6383944e+00
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (30 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 4.01323e+00 on atom 1
40: F-Norm = 1.63839e+00
40:
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
40: Potential Energy = -9.9064207e-01
40: Maximum force = 2.5781622e+00 on atom 1
40: Norm of force = 1.0525302e+00
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (31 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40:
40: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40:
40: There was 1 warning
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (single precision)
40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
40:
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Low-Memory BFGS Minimizer:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: Using 10 BFGS correction steps.
40:
40: F-max = 4.01323e+00 on atom 1
40: F-Norm = 1.63839e+00
40:
40:
40: writing lowest energy coordinates.
40:
40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
40: Potential Energy = -9.9064207e-01
40: Maximum force = 2.5781622e+00 on atom 1
40: Norm of force = 1.0525302e+00
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (30 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 3.1939697e+02
40: Maximum force = 9.9704248e+03 on atom 9
40: Norm of force = 4.6227540e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (447 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (single precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 2.41672e+04 on atom 10
40: F-Norm = 1.19357e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 1.5625757e+02
40: Maximum force = 7.5018242e+03 on atom 9
40: Norm of force = 3.6139019e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (489 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40:
40: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40:
40: There was 1 warning
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (single precision)
40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
40:
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Low-Memory BFGS Minimizer:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: Using 10 BFGS correction steps.
40:
40: F-max = 2.41672e+04 on atom 10
40: F-Norm = 1.19357e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 5.6111725e+02
40: Maximum force = 1.2685491e+04 on atom 10
40: Norm of force = 6.0643622e+03
40: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (477 ms)
40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1504 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 21 tests from 7 test cases ran. (46866 ms total)
40: [ PASSED ] 21 tests.
40:
40: YOU HAVE 4 DISABLED TESTS
40:
40/40 Test #40: MdrunMpiTests .................... Passed 46.91 sec
100% tests passed, 0 tests failed out of 40
Label Time Summary:
GTest = 262.22 sec*proc (40 tests)
IntegrationTest = 130.76 sec*proc (5 tests)
MpiTest = 0.54 sec*proc (3 tests)
SlowTest = 115.56 sec*proc (1 test)
UnitTest = 15.90 sec*proc (34 tests)
Total Test time (real) = 262.56 sec
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
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[ 79%] Built target libgromacs
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void {anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::SettleTest_SatisfiesConstraints_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target applied-forces-test
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target listed-forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target mdrun-mpi-test
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
updateGroupsCog.addCogs(globalAtomIndices, positions);
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target domdec-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
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cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target fft-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:97:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:165:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:174:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target hardware-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target commandline-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
In file included from /usr/include/c++/8/map:61,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:47:
/usr/include/c++/8/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::map(std::initializer_list<std::pair<const _Key, _Tp> >, const _Compare&, const allocator_type&) [with _Key = gmx::BasicVector<int>; _Tp = t_complex; _Compare = std::less<gmx::BasicVector<int> >; _Alloc = std::allocator<std::pair<const gmx::BasicVector<int>, t_complex> >]':
/usr/include/c++/8/bits/stl_map.h:226:7: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
map(initializer_list<value_type> __l,
^~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void runTest(const gmx_gpu_info_t &gpuInfo,
^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void runTest(const gmx_gpu_info_t &gpuInfo,
^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
vector(_InputIterator __first, _InputIterator __last,
^~~~~~
/usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 83%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:326:114: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates1(c_sampleCoordinatesFull.begin(), c_sampleCoordinatesFull.begin() + 1);
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:118: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates2(c_sampleCoordinatesFull.begin() + 1, c_sampleCoordinatesFull.begin() + 3);
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:330:120: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates13(c_sampleCoordinatesFull.begin() + 3, c_sampleCoordinatesFull.begin() + 16);
^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target ewald-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
^~~~~~~~~~~~~~~~~
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/bits/random.h:34,
from /usr/include/c++/8/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target random-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target table-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target utility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target compat-test
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target awh-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx-test
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/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_QuasiHarmonic_300_NoLinear_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_Schlitter_300_NoLinear_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_Schlitter_300_Linear_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_QuasiHarmonic_200_NoLinear_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::Entropy_QuasiHarmonic_200_Linear_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target pdb2gmx-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target gmxana-test
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target utility-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
Scanning dependencies of target trajectoryanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target energyanalysis-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report-methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
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cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target legacy-mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target legacy-mdrun-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_Computes100Points_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_Computes100PointsWithRectangularPBC_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::SurfaceAreaTest_Computes100PointsWithTriclinicPBC_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target trajectoryanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target selection-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (9 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (21 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (3 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariants
1: [ OK ] ReferenceDataTest.HandlesVariants (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms)
1: [----------] 34 tests from ReferenceDataTest (43 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (1 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (3 ms)
1: [----------] 4 tests from XvgTests (9 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (74 ms total)
1: [ PASSED ] 59 tests.
1/40 Test #1: TestUtilsUnitTests ............... Passed 0.58 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (2 ms total)
2: [ PASSED ] 1 test.
2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.06 sec
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3: [==========] Running 50 tests from 8 test cases.
3: [----------] Global test environment set-up.
3: [----------] 1 test from VerletBufferConstraintTest
3: [ RUN ] VerletBufferConstraintTest.EqualMasses
3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
3: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
3:
3: [----------] 3 tests from PrintEbin
3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (2 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (2 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (1 ms)
3: [----------] 3 tests from PrintEbin (5 ms total)
3:
3: [----------] 4 tests from ShakeTest
3: [ RUN ] ShakeTest.ConstrainsOneBond
3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
3: [----------] 4 tests from ShakeTest (0 ms total)
3:
3: [----------] 1 test from NullSignalTest
3: [ RUN ] NullSignalTest.NullSignallerWorks
3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
3: [----------] 1 test from NullSignalTest (0 ms total)
3:
3: [----------] 7 tests from SignalTest
3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
3: [----------] 7 tests from SignalTest (0 ms total)
3:
3: [----------] 9 tests from UpdateGroups
3: [ RUN ] UpdateGroups.ethaneUA
3: [ OK ] UpdateGroups.ethaneUA (0 ms)
3: [ RUN ] UpdateGroups.methane
3: [ OK ] UpdateGroups.methane (0 ms)
3: [ RUN ] UpdateGroups.ethane
3: [ OK ] UpdateGroups.ethane (0 ms)
3: [ RUN ] UpdateGroups.butaneUA
3: [ OK ] UpdateGroups.butaneUA (0 ms)
3: [ RUN ] UpdateGroups.waterThreeSite
3: [ OK ] UpdateGroups.waterThreeSite (0 ms)
3: [ RUN ] UpdateGroups.waterFourSite
3: [ OK ] UpdateGroups.waterFourSite (0 ms)
3: [ RUN ] UpdateGroups.fourAtomsWithSettle
3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
3: [ RUN ] UpdateGroups.waterFlexAngle
3: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
3: [ RUN ] UpdateGroups.twoMoltypes
3: [ OK ] UpdateGroups.twoMoltypes (0 ms)
3: [----------] 9 tests from UpdateGroups (1 ms total)
3:
3: [----------] 1 test from UpdateGroupsCog
3: [ RUN ] UpdateGroupsCog.ComputesCogs
3: [ OK ] UpdateGroupsCog.ComputesCogs (3 ms)
3: [----------] 1 test from UpdateGroupsCog (4 ms total)
3:
3: [----------] 24 tests from WithParameters/SettleTest
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (1 ms)
3: [----------] 24 tests from WithParameters/SettleTest (4 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 50 tests from 8 test cases ran. (17 ms total)
3: [ PASSED ] 50 tests.
3/40 Test #3: MdlibUnitTest .................... Passed 0.08 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4: [==========] Running 3 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 3 tests from ElectricFieldTest
4: [ RUN ] ElectricFieldTest.Static
4: [ OK ] ElectricFieldTest.Static (1 ms)
4: [ RUN ] ElectricFieldTest.Oscillating
4: [ OK ] ElectricFieldTest.Oscillating (1 ms)
4: [ RUN ] ElectricFieldTest.Pulsed
4: [ OK ] ElectricFieldTest.Pulsed (0 ms)
4: [----------] 3 tests from ElectricFieldTest (2 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 3 tests from 1 test case ran. (2 ms total)
4: [ PASSED ] 3 tests.
4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.06 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 15 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 15 tests from BondedTest
5: [ RUN ] BondedTest.BondAnglePbcNone
5: [ OK ] BondedTest.BondAnglePbcNone (1 ms)
5: [ RUN ] BondedTest.BondAnglePbcXy
5: [ OK ] BondedTest.BondAnglePbcXy (1 ms)
5: [ RUN ] BondedTest.BondAnglePbcXyz
5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcNone
5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXy
5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXyz
5: [ OK ] BondedTest.DihedralAnglePbcXyz (1 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcNo
5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXy
5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXyz
5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcNo
5: [ OK ] BondedTest.IfuncAnglesPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXy
5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ
5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo
5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (1 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms)
5: [----------] 15 tests from BondedTest (5 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 15 tests from 1 test case ran. (5 ms total)
5: [ PASSED ] 15 tests.
5/40 Test #5: ListedForcesTest ................. Passed 0.05 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6: [==========] Running 55 tests from 6 test cases.
6: [----------] Global test environment set-up.
6: [----------] 3 tests from CommandLineHelpModuleTest
6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (103 ms)
6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (7 ms)
6: [----------] 3 tests from CommandLineHelpModuleTest (111 ms total)
6:
6: [----------] 6 tests from CommandLineHelpWriterTest
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
6: [----------] 6 tests from CommandLineHelpWriterTest (9 ms total)
6:
6: [----------] 6 tests from CommandLineModuleManagerTest
6: [ RUN ] CommandLineModuleManagerTest.RunsModule
6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
6: [----------] 6 tests from CommandLineModuleManagerTest (4 ms total)
6:
6: [----------] 13 tests from CommandLineParserTest
6: [ RUN ] CommandLineParserTest.HandlesSingleValues
6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesString
6: [ OK ] CommandLineParserTest.HandlesString (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
6: [----------] 13 tests from CommandLineParserTest (3 ms total)
6:
6: [----------] 6 tests from CommandLineProgramContextTest
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
6:
6: [----------] 21 tests from ParseCommonArgsTest
6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (4 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
6: [----------] 21 tests from ParseCommonArgsTest (18 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 55 tests from 6 test cases ran. (148 ms total)
6: [ PASSED ] 55 tests.
6/40 Test #6: CommandLineUnitTests ............. Passed 0.19 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 9 tests from 2 test cases.
7: [----------] Global test environment set-up.
7: [----------] 7 tests from HashedMap
7: [ RUN ] HashedMap.InsertsFinds
7: [ OK ] HashedMap.InsertsFinds (0 ms)
7: [ RUN ] HashedMap.NegativeKeysWork
7: [ OK ] HashedMap.NegativeKeysWork (0 ms)
7: [ RUN ] HashedMap.InsertsErases
7: [ OK ] HashedMap.InsertsErases (0 ms)
7: [ RUN ] HashedMap.InsertsOrAssigns
7: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
7: [ RUN ] HashedMap.Clears
7: [ OK ] HashedMap.Clears (0 ms)
7: [ RUN ] HashedMap.LinkedEntries
7: [ OK ] HashedMap.LinkedEntries (0 ms)
7: [ RUN ] HashedMap.ResizesTable
7: [ OK ] HashedMap.ResizesTable (0 ms)
7: [----------] 7 tests from HashedMap (0 ms total)
7:
7: [----------] 2 tests from LocalAtomSetManager
7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (1 ms)
7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
7: [----------] 2 tests from LocalAtomSetManager (1 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 9 tests from 2 test cases ran. (2 ms total)
7: [ PASSED ] 9 tests.
7/40 Test #7: DomDecTests ...................... Passed 0.06 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 257 tests from 10 test cases.
8: [----------] Global test environment set-up.
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (23 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (24 ms total)
8:
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (28 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (23 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (24 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (23 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (29 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (31 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (32 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (31 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (34 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (35 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (33 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (28 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (42 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (27 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (29 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (30 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (31 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (27 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (28 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (28 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (28 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (29 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (29 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (29 ms)
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (723 ms total)
8:
8: [----------] 144 tests from SaneInput/PmeGatherTest
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
8: [----------] 144 tests from SaneInput/PmeGatherTest (236 ms total)
8:
8: [----------] 16 tests from SaneInput/PmeSolveTest
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (7 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (8 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (8 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (8 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (10 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (9 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (5 ms)
8: [----------] 16 tests from SaneInput/PmeSolveTest (97 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (32 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (9 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (9 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (9 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (5 ms)
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (55 ms total)
8:
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (9 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (8 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (9 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (9 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (5 ms)
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (89 ms total)
8:
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (9 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (8 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (79 ms total)
8:
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (10 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (12 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (14 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (10 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (11 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (14 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (15 ms)
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (123 ms total)
8:
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (16 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (17 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (25 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (27 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (45 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (50 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (18 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (20 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (27 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (30 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (32 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (42 ms)
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (372 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 257 tests from 10 test cases ran. (1865 ms total)
8: [ PASSED ] 257 tests.
8/40 Test #8: EwaldUnitTests ................... Passed 2.08 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 14 tests from 4 test cases.
9: [----------] Global test environment set-up.
9: [----------] 2 tests from ManyFFTTest
9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (27 ms)
9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (44 ms)
9: [----------] 2 tests from ManyFFTTest (75 ms total)
9:
9: [----------] 1 test from FFTTest
9: [ RUN ] FFTTest.Real2DLength18_15Test
9: [ OK ] FFTTest.Real2DLength18_15Test (13 ms)
9: [----------] 1 test from FFTTest (13 ms total)
9:
9: [----------] 1 test from FFFTest3D
9: [ RUN ] FFFTest3D.Real5_6_9
9: [ OK ] FFFTest3D.Real5_6_9 (10 ms)
9: [----------] 1 test from FFFTest3D (12 ms total)
9:
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (4 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (6 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (7 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (23 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (34 ms)
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (91 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 14 tests from 4 test cases ran. (195 ms total)
9: [ PASSED ] 14 tests.
9/40 Test #9: FFTUnitTests ..................... Passed 0.28 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 60 tests from 19 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/1 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Swap
10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Comparison
10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Swap
10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Comparison
10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Swap
10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Comparison
10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Swap
10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Comparison
10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (1 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
10:
10: [----------] 1 test from HostAllocatorUntypedTest
10: [ RUN ] HostAllocatorUntypedTest.Comparison
10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
10:
10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/0 (2 ms total)
10:
10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (2 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/2 (3 ms total)
10:
10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 60 tests from 19 test cases ran. (11 ms total)
10: [ PASSED ] 60 tests.
10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.08 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 4 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 4 tests from HardwareTopologyTest
11: [ RUN ] HardwareTopologyTest.Execute
11: [ OK ] HardwareTopologyTest.Execute (28 ms)
11: [ RUN ] HardwareTopologyTest.HwlocExecute
11: [ OK ] HardwareTopologyTest.HwlocExecute (29 ms)
11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (32 ms)
11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (30 ms)
11: [----------] 4 tests from HardwareTopologyTest (119 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 4 tests from 1 test case ran. (120 ms total)
11: [ PASSED ] 4 tests.
11/40 Test #11: HardwareUnitTests ................ Passed 0.18 sec
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 112 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from EmptyArrayRefWithPaddingTest
12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyArrayRefWithPaddingTest (1 ms total)
12:
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (1 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (1 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (1 ms total)
12:
12: [----------] 6 tests from StructureSimilarityTest
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
12: [----------] 6 tests from StructureSimilarityTest (2 ms total)
12:
12: [----------] 21 tests from FunctionTest
12: [ RUN ] FunctionTest.StaticLog2
12: [ OK ] FunctionTest.StaticLog2 (1 ms)
12: [ RUN ] FunctionTest.Log2I32Bit
12: [ OK ] FunctionTest.Log2I32Bit (1 ms)
12: [ RUN ] FunctionTest.Log2I64Bit
12: [ OK ] FunctionTest.Log2I64Bit (1 ms)
12: [ RUN ] FunctionTest.GreatestCommonDivisor
12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
12: [ RUN ] FunctionTest.InvsqrtFloat
12: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
12: [ RUN ] FunctionTest.InvsqrtDouble
12: [ OK ] FunctionTest.InvsqrtDouble (1 ms)
12: [ RUN ] FunctionTest.InvsqrtInteger
12: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
12: [ RUN ] FunctionTest.InvcbrtFloat
12: [ OK ] FunctionTest.InvcbrtFloat (1 ms)
12: [ RUN ] FunctionTest.InvcbrtDouble
12: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
12: [ RUN ] FunctionTest.InvcbrtInteger
12: [ OK ] FunctionTest.InvcbrtInteger (1 ms)
12: [ RUN ] FunctionTest.SixthrootFloat
12: [ OK ] FunctionTest.SixthrootFloat (1 ms)
12: [ RUN ] FunctionTest.SixthrootDouble
12: [ OK ] FunctionTest.SixthrootDouble (1 ms)
12: [ RUN ] FunctionTest.SixthrootInteger
12: [ OK ] FunctionTest.SixthrootInteger (1 ms)
12: [ RUN ] FunctionTest.InvsixthrootFloat
12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootDouble
12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootInteger
12: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
12: [ RUN ] FunctionTest.Powers
12: [ OK ] FunctionTest.Powers (0 ms)
12: [ RUN ] FunctionTest.ErfInvFloat
12: [ OK ] FunctionTest.ErfInvFloat (1 ms)
12: [ RUN ] FunctionTest.ErfInvDouble
12: [ OK ] FunctionTest.ErfInvDouble (0 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (2 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
12: [----------] 21 tests from FunctionTest (19 ms total)
12:
12: [----------] 2 tests from InvertMatrixTest
12: [ RUN ] InvertMatrixTest.IdentityIsImpotent
12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertMatrixTest.ComputesInverse
12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
12: [----------] 2 tests from InvertMatrixTest (1 ms total)
12:
12: [----------] 2 tests from InvertBoxMatrixTest
12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
12: [----------] 2 tests from InvertBoxMatrixTest (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanCopyAssign
12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanMoveAssign
12: [ OK ] PaddedVectorTest/0.CanMoveAssign (1 ms)
12: [ RUN ] PaddedVectorTest/0.CanSwap
12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (1 ms)
12: [ RUN ] PaddedVectorTest/1.CanCopyAssign
12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanMoveAssign
12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanSwap
12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/1 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanCopyAssign
12: [ OK ] PaddedVectorTest/2.CanCopyAssign (1 ms)
12: [ RUN ] PaddedVectorTest/2.CanMoveAssign
12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanSwap
12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/2 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanCopyAssign
12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanMoveAssign
12: [ OK ] PaddedVectorTest/3.CanMoveAssign (1 ms)
12: [ RUN ] PaddedVectorTest/3.CanSwap
12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/3 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanCopyAssign
12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanMoveAssign
12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanSwap
12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/4 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanCopyAssign
12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanMoveAssign
12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanSwap
12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanCopyAssign
12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanMoveAssign
12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanSwap
12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanCopyAssign
12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanMoveAssign
12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanSwap
12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanCopyAssign
12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanMoveAssign
12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanSwap
12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanCopyAssign
12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanMoveAssign
12: [ OK ] PaddedVectorTest/9.CanMoveAssign (1 ms)
12: [ RUN ] PaddedVectorTest/9.CanSwap
12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total)
12:
12: [----------] 33 tests from RVecTest
12: [ RUN ] RVecTest.CanBeStoredInVector
12: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAsMutable_rvec
12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Array
12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
12: [ RUN ] RVecTest.CanAddRVecToRvec
12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanAddAssignRVecToRvec
12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractRVecFromRvec
12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanDotProductRVecByRvec
12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanCrossProductRVecByRvec
12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVecInplace
12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
12: [ RUN ] RVecTest.CanScaleRVec
12: [ OK ] RVecTest.CanScaleRVec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVec
12: [ OK ] RVecTest.CanDivideRVec (0 ms)
12: [ RUN ] RVecTest.CanDoUnitvFromRVec
12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanSqLengthOfRVec
12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanLengthOfRVec
12: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToRVec
12: [ OK ] RVecTest.CanCastToRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToDVec
12: [ OK ] RVecTest.CanCastToDVec (0 ms)
12: [ RUN ] RVecTest.CanLeftScalarMultiply
12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanRightScalarMultiply
12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanGetUnitvFromRVec
12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanGetSqLengthOfRVec
12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanGetLengthOfRVec
12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoCrossProductOfRVec
12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoDotProductOfRVec
12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
12: [ RUN ] RVecTest.WorksAs_dvec_Reference
12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_ivec_Reference
12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Reference
12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
12: [ RUN ] RVecTest.CopyConstructorWorks
12: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
12: [ RUN ] RVecTest.CopyAssignmentWorks
12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
12: [ RUN ] RVecTest.MoveConstructorWorks
12: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
12: [ RUN ] RVecTest.MoveAssignmentWorks
12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
12: [----------] 33 tests from RVecTest (2 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 112 tests from 20 test cases ran. (40 ms total)
12: [ PASSED ] 112 tests.
12/40 Test #12: MathUnitTests .................... Passed 0.12 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 17 tests from ThreadAffinityTest
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
13: NOTE: Affinity setting failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
13: NOTE: Affinity setting for 1/2 threads failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
13: [----------] 17 tests from ThreadAffinityTest (18 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 1 test case ran. (18 ms total)
13: [ PASSED ] 17 tests.
13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.08 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 13 tests from 2 test cases.
14: [----------] Global test environment set-up.
14: [----------] 6 tests from ThreadAffinityMultiRankTest
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (10 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (8 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (6 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (12 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (11 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (10 ms)
14: [----------] 6 tests from ThreadAffinityMultiRankTest (57 ms total)
14:
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (21 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (10 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (10 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (10 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (10 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (69 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (10 ms)
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (140 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 13 tests from 2 test cases ran. (197 ms total)
14: [ PASSED ] 13 tests.
14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.26 sec
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 22 tests from 4 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from TextTableFormatterTest
15: [ RUN ] TextTableFormatterTest.HandlesBasicCase
15: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesIndentation
15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
15: [----------] 6 tests from TextTableFormatterTest (4 ms total)
15:
15: [----------] 3 tests from HelpManagerTest
15: [ RUN ] HelpManagerTest.HandlesRootTopic
15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
15: [ RUN ] HelpManagerTest.HandlesSubTopics
15: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
15: [ RUN ] HelpManagerTest.HandlesInvalidTopics
15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
15: [----------] 3 tests from HelpManagerTest (1 ms total)
15:
15: [----------] 2 tests from HelpTopicFormattingTest
15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
15: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
15:
15: [----------] 11 tests from HelpWriterContextTest
15: [ RUN ] HelpWriterContextTest.FormatsParagraphs
15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralText
15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsBulletList
15: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsGridTable
15: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsTitles
15: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
15: [----------] 11 tests from HelpWriterContextTest (6 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 22 tests from 4 test cases ran. (13 ms total)
15: [ PASSED ] 22 tests.
15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.07 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 110 tests from 18 test cases.
16: [----------] Global test environment set-up.
16: [----------] 5 tests from AbstractOptionStorageTest
16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
16: [----------] 5 tests from AbstractOptionStorageTest (3 ms total)
16:
16: [----------] 8 tests from FileNameOptionTest
16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
16: [----------] 8 tests from FileNameOptionTest (1 ms total)
16:
16: [----------] 15 tests from FileNameOptionManagerTest
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (1 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (1 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
16: [----------] 15 tests from FileNameOptionManagerTest (3 ms total)
16:
16: [----------] 1 test from OptionsTest
16: [ RUN ] OptionsTest.FailsOnNonsafeStorage
16: [ OK ] OptionsTest.FailsOnNonsafeStorage (1 ms)
16: [----------] 1 test from OptionsTest (1 ms total)
16:
16: [----------] 9 tests from OptionsAssignerTest
16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMissingValue
16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesExtraValue
16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesGroups
16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesSections
16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
16: [----------] 9 tests from OptionsAssignerTest (1 ms total)
16:
16: [----------] 4 tests from OptionsAssignerBooleanTest
16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
16:
16: [----------] 13 tests from OptionsAssignerIntegerTest
16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (1 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
16: [----------] 13 tests from OptionsAssignerIntegerTest (2 ms total)
16:
16: [----------] 5 tests from OptionsAssignerDoubleTest
16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (1 ms)
16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
16:
16: [----------] 9 tests from OptionsAssignerStringTest
16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (1 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 9 tests from OptionsAssignerStringTest (2 ms total)
16:
16: [----------] 6 tests from OptionsAssignerEnumTest
16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
16:
16: [----------] 8 tests from RepeatingOptionSectionTest
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (1 ms)
16: [----------] 8 tests from RepeatingOptionSectionTest (2 ms total)
16:
16: [----------] 1 test from TimeUnitManagerTest
16: [ RUN ] TimeUnitManagerTest.BasicOperations
16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
16: [----------] 1 test from TimeUnitManagerTest (0 ms total)
16:
16: [----------] 4 tests from TimeUnitBehaviorTest
16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (1 ms)
16: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
16:
16: [----------] 2 tests from TreeValueSupportAssignTest
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
16:
16: [----------] 1 test from TreeValueSupportAssignErrorTest
16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (1 ms)
16: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total)
16:
16: [----------] 5 tests from TreeValueSupportCheckTest
16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
16: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total)
16:
16: [----------] 6 tests from TreeValueSupportAdjustTest
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
16: [----------] 6 tests from TreeValueSupportAdjustTest (3 ms total)
16:
16: [----------] 8 tests from TreeValueSupportTest
16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsInt64Option
16: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsStringOption
16: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsFloatOption
16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumOption
16: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
16: [----------] 8 tests from TreeValueSupportTest (7 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 110 tests from 18 test cases ran. (31 ms total)
16: [ PASSED ] 110 tests.
16/40 Test #16: OptionsUnitTests ................. Passed 0.10 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 44 tests from 10 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from ExponentialDistributionTest
17: [ RUN ] ExponentialDistributionTest.Output
17: [ OK ] ExponentialDistributionTest.Output (1 ms)
17: [ RUN ] ExponentialDistributionTest.Logical
17: [ OK ] ExponentialDistributionTest.Logical (0 ms)
17: [ RUN ] ExponentialDistributionTest.Reset
17: [ OK ] ExponentialDistributionTest.Reset (0 ms)
17: [ RUN ] ExponentialDistributionTest.AltParam
17: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
17:
17: [----------] 4 tests from GammaDistributionTest
17: [ RUN ] GammaDistributionTest.Output
17: [ OK ] GammaDistributionTest.Output (1 ms)
17: [ RUN ] GammaDistributionTest.Logical
17: [ OK ] GammaDistributionTest.Logical (0 ms)
17: [ RUN ] GammaDistributionTest.Reset
17: [ OK ] GammaDistributionTest.Reset (0 ms)
17: [ RUN ] GammaDistributionTest.AltParam
17: [ OK ] GammaDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from GammaDistributionTest (1 ms total)
17:
17: [----------] 4 tests from NormalDistributionTest
17: [ RUN ] NormalDistributionTest.Output
17: [ OK ] NormalDistributionTest.Output (1 ms)
17: [ RUN ] NormalDistributionTest.Logical
17: [ OK ] NormalDistributionTest.Logical (0 ms)
17: [ RUN ] NormalDistributionTest.Reset
17: [ OK ] NormalDistributionTest.Reset (0 ms)
17: [ RUN ] NormalDistributionTest.AltParam
17: [ OK ] NormalDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from NormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from SeedTest
17: [ RUN ] SeedTest.makeRandomSeed
17: [ OK ] SeedTest.makeRandomSeed (0 ms)
17: [----------] 1 test from SeedTest (1 ms total)
17:
17: [----------] 6 tests from TabulatedNormalDistributionTest
17: [ RUN ] TabulatedNormalDistributionTest.Output14
17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Output16
17: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Logical
17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Reset
17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.AltParam
17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
17: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from TabulatedNormalDistributionTableTest
17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (9 ms)
17: [----------] 1 test from TabulatedNormalDistributionTableTest (9 ms total)
17:
17: [----------] 6 tests from ThreeFry2x64Test
17: [ RUN ] ThreeFry2x64Test.Logical
17: [ OK ] ThreeFry2x64Test.Logical (0 ms)
17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
17: [ RUN ] ThreeFry2x64Test.Reseed
17: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
17: [ RUN ] ThreeFry2x64Test.Discard
17: [ OK ] ThreeFry2x64Test.Discard (0 ms)
17: [ RUN ] ThreeFry2x64Test.InvalidCounter
17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
17: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
17:
17: [----------] 4 tests from UniformIntDistributionTest
17: [ RUN ] UniformIntDistributionTest.Output
17: [ OK ] UniformIntDistributionTest.Output (0 ms)
17: [ RUN ] UniformIntDistributionTest.Logical
17: [ OK ] UniformIntDistributionTest.Logical (0 ms)
17: [ RUN ] UniformIntDistributionTest.Reset
17: [ OK ] UniformIntDistributionTest.Reset (0 ms)
17: [ RUN ] UniformIntDistributionTest.AltParam
17: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
17:
17: [----------] 5 tests from UniformRealDistributionTest
17: [ RUN ] UniformRealDistributionTest.GenerateCanonical
17: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
17: [ RUN ] UniformRealDistributionTest.Output
17: [ OK ] UniformRealDistributionTest.Output (0 ms)
17: [ RUN ] UniformRealDistributionTest.Logical
17: [ OK ] UniformRealDistributionTest.Logical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Reset
17: [ OK ] UniformRealDistributionTest.Reset (0 ms)
17: [ RUN ] UniformRealDistributionTest.AltParam
17: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
17: [----------] 5 tests from UniformRealDistributionTest (2 ms total)
17:
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 44 tests from 10 test cases ran. (21 ms total)
17: [ PASSED ] 44 tests.
17/40 Test #17: RandomUnitTests .................. Passed 0.12 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 1 test from 1 test case.
18: [----------] Global test environment set-up.
18: [----------] 1 test from RestraintManager
18: [ RUN ] RestraintManager.restraintList
18: [ OK ] RestraintManager.restraintList (0 ms)
18: [----------] 1 test from RestraintManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 1 test from 1 test case ran. (1 ms total)
18: [ PASSED ] 1 test.
18/40 Test #18: RestraintTests ................... Passed 0.05 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 16 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (8 ms)
19: [ RUN ] SplineTableTest/0.Sinc
19: [ OK ] SplineTableTest/0.Sinc (4 ms)
19: [ RUN ] SplineTableTest/0.LJ12
19: [ OK ] SplineTableTest/0.LJ12 (150 ms)
19: [ RUN ] SplineTableTest/0.PmeCorrection
19: [ OK ] SplineTableTest/0.PmeCorrection (9 ms)
19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (7 ms)
19: [ RUN ] SplineTableTest/0.TwoFunctions
19: [ OK ] SplineTableTest/0.TwoFunctions (277 ms)
19: [ RUN ] SplineTableTest/0.ThreeFunctions
19: [ OK ] SplineTableTest/0.ThreeFunctions (358 ms)
19: [----------] 8 tests from SplineTableTest/0 (815 ms total)
19:
19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (11 ms)
19: [ RUN ] SplineTableTest/1.Sinc
19: [ OK ] SplineTableTest/1.Sinc (9 ms)
19: [ RUN ] SplineTableTest/1.LJ12
19: [ OK ] SplineTableTest/1.LJ12 (347 ms)
19: [ RUN ] SplineTableTest/1.PmeCorrection
19: [ OK ] SplineTableTest/1.PmeCorrection (7 ms)
19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms)
19: [ RUN ] SplineTableTest/1.TwoFunctions
19: [ OK ] SplineTableTest/1.TwoFunctions (694 ms)
19: [ RUN ] SplineTableTest/1.ThreeFunctions
19: [ OK ] SplineTableTest/1.ThreeFunctions (822 ms)
19: [----------] 8 tests from SplineTableTest/1 (1899 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 16 tests from 2 test cases ran. (2715 ms total)
19: [ PASSED ] 16 tests.
19/40 Test #19: TableUnitTests ................... Passed 2.77 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 1 test case.
20: [----------] Global test environment set-up.
20: [----------] 3 tests from GpuIdStringHandlingTest
20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork
20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (1 ms)
20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid
20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow
20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms)
20: [----------] 3 tests from GpuIdStringHandlingTest (2 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 1 test case ran. (2 ms total)
20: [ PASSED ] 3 tests.
20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.06 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 325 tests from 52 test cases.
21: [----------] Global test environment set-up.
21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (2 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.Move
21: [ OK ] AllocatorTest/0.Move (0 ms)
21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/0 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (2 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.Move
21: [ OK ] AllocatorTest/1.Move (0 ms)
21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/1 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.Move
21: [ OK ] AllocatorTest/2.Move (0 ms)
21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/2 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.Move
21: [ OK ] AllocatorTest/3.Move (0 ms)
21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/3 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (3 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/4.Move
21: [ OK ] AllocatorTest/4.Move (0 ms)
21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/4 (4 ms total)
21:
21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (3 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.Move
21: [ OK ] AllocatorTest/5.Move (0 ms)
21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/5 (4 ms total)
21:
21: [----------] 1 test from AllocatorUntypedTest
21: [ RUN ] AllocatorUntypedTest.Comparison
21: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
21: [----------] 1 test from AllocatorUntypedTest (0 ms total)
21:
21: [----------] 1 test from EmptyArrayRefTest
21: [ RUN ] EmptyArrayRefTest.IsEmpty
21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyArrayRefTest (0 ms total)
21:
21: [----------] 1 test from EmptyConstArrayRefTest
21: [ RUN ] EmptyConstArrayRefTest.IsEmpty
21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/3 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/18 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
21: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
21:
21: [----------] 4 tests from KeyValueTreeSerializerTest
21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
21: [----------] 4 tests from KeyValueTreeSerializerTest (3 ms total)
21:
21: [----------] 6 tests from TreeValueTransformTest
21: [ RUN ] TreeValueTransformTest.SimpleTransforms
21: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromString
21: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
21: [ RUN ] TreeValueTransformTest.ScopedTransformRules
21: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
21: [----------] 6 tests from TreeValueTransformTest (4 ms total)
21:
21: [----------] 1 test from TreeValueTransformErrorTest
21: [ RUN ] TreeValueTransformErrorTest.ConversionError
21: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
21: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
21:
21: [----------] 2 tests from RegexBasicTest
21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported
21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (2 ms)
21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported
21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (2 ms)
21: [----------] 2 tests from RegexBasicTest (4 ms total)
21:
21: [----------] 5 tests from LoggerTest
21: [ RUN ] LoggerTest.EmptyLoggerWorks
21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
21: [ RUN ] LoggerTest.LogsToStream
21: [ OK ] LoggerTest.LogsToStream (1 ms)
21: [ RUN ] LoggerTest.LogsToFile
21: [ OK ] LoggerTest.LogsToFile (2 ms)
21: [ RUN ] LoggerTest.LevelFilteringWorks
21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
21: [ RUN ] LoggerTest.LogsToMultipleStreams
21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
21: [----------] 5 tests from LoggerTest (4 ms total)
21:
21: [----------] 4 tests from MutexBasicTest
21: [ RUN ] MutexBasicTest.CanBeMade
21: [ OK ] MutexBasicTest.CanBeMade (0 ms)
21: [ RUN ] MutexBasicTest.CanBeLocked
21: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeTryLocked
21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
21: [----------] 4 tests from MutexBasicTest (0 ms total)
21:
21: [----------] 3 tests from MutexTaskTest
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
21: [----------] 3 tests from MutexTaskTest (2 ms total)
21:
21: [----------] 4 tests from PathTest
21: [ RUN ] PathTest.StripSourcePrefixWorks
21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks
21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathWorks
21: [ OK ] PathTest.GetParentPathWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathAndBasenameWorks
21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms)
21: [----------] 4 tests from PathTest (0 ms total)
21:
21: [----------] 2 tests from PhysicalNodeCommunicatorTest
21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
21:
21: [----------] 7 tests from StringUtilityTest
21: [ RUN ] StringUtilityTest.StartsWith
21: [ OK ] StringUtilityTest.StartsWith (1 ms)
21: [ RUN ] StringUtilityTest.EndsWith
21: [ OK ] StringUtilityTest.EndsWith (0 ms)
21: [ RUN ] StringUtilityTest.StripSuffixIfPresent
21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
21: [ RUN ] StringUtilityTest.StripString
21: [ OK ] StringUtilityTest.StripString (0 ms)
21: [ RUN ] StringUtilityTest.SplitString
21: [ OK ] StringUtilityTest.SplitString (0 ms)
21: [ RUN ] StringUtilityTest.SplitDelimitedString
21: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
21: [----------] 7 tests from StringUtilityTest (3 ms total)
21:
21: [----------] 2 tests from FormatStringTest
21: [ RUN ] FormatStringTest.HandlesBasicFormatting
21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
21: [ RUN ] FormatStringTest.HandlesLongStrings
21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
21: [----------] 2 tests from FormatStringTest (1 ms total)
21:
21: [----------] 1 test from StringFormatterTest
21: [ RUN ] StringFormatterTest.HandlesBasicFormatting
21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
21: [----------] 1 test from StringFormatterTest (0 ms total)
21:
21: [----------] 1 test from formatAndJoinTest
21: [ RUN ] formatAndJoinTest.Works
21: [ OK ] formatAndJoinTest.Works (0 ms)
21: [----------] 1 test from formatAndJoinTest (0 ms total)
21:
21: [----------] 1 test from JoinStringsTest
21: [ RUN ] JoinStringsTest.Works
21: [ OK ] JoinStringsTest.Works (0 ms)
21: [----------] 1 test from JoinStringsTest (0 ms total)
21:
21: [----------] 6 tests from ReplaceAllTest
21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesNoMatches
21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
21: [----------] 6 tests from ReplaceAllTest (1 ms total)
21:
21: [----------] 10 tests from TextLineWrapperTest
21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectly
21: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndent
21: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
21: [----------] 10 tests from TextLineWrapperTest (3 ms total)
21:
21: [----------] 6 tests from TextWriterTest
21: [ RUN ] TextWriterTest.WritesLines
21: [ OK ] TextWriterTest.WritesLines (1 ms)
21: [ RUN ] TextWriterTest.WritesLinesInParts
21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
21: [ RUN ] TextWriterTest.WritesWrappedLines
21: [ OK ] TextWriterTest.WritesWrappedLines (1 ms)
21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
21: [ RUN ] TextWriterTest.TracksNewlines
21: [ OK ] TextWriterTest.TracksNewlines (0 ms)
21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (1 ms)
21: [----------] 6 tests from TextWriterTest (3 ms total)
21:
21: [----------] 1 test from TypeTraitsTest
21: [ RUN ] TypeTraitsTest.IsIntegralConstant
21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
21: [----------] 1 test from TypeTraitsTest (0 ms total)
21:
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
21:
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
21:
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
21:
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (3 ms total)
21:
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 325 tests from 52 test cases ran. (66 ms total)
21: [ PASSED ] 325 tests.
21/40 Test #21: UtilityUnitTests ................. Passed 0.18 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 2 tests from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from PhysicalNodeCommunicatorTest
22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (3 ms)
22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (19 ms)
22: [----------] 2 tests from PhysicalNodeCommunicatorTest (22 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 2 tests from 1 test case ran. (23 ms total)
22: [ PASSED ] 2 tests.
22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.08 sec
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 17 tests from 4 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from FileMD5Test
23: [ RUN ] FileMD5Test.CanComputeMD5
23: [ OK ] FileMD5Test.CanComputeMD5 (9 ms)
23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
23: [----------] 2 tests from FileMD5Test (10 ms total)
23:
23: [----------] 9 tests from ReadTest
23: [ RUN ] ReadTest.get_eint_ReadsInteger
23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (1 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_eint64_ReadsInteger
23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsInteger
23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsFloat
23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
23: [ RUN ] ReadTest.get_ereal_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not a
23: real value
23:
23:
23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
23: [----------] 9 tests from ReadTest (1 ms total)
23:
23: [----------] 2 tests from TngTest
23: [ RUN ] TngTest.CanOpenTngFile
23: [ OK ] TngTest.CanOpenTngFile (1 ms)
23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
23: [----------] 2 tests from TngTest (1 ms total)
23:
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (5 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (13 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms)
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (23 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 17 tests from 4 test cases ran. (36 ms total)
23: [ PASSED ] 17 tests.
23/40 Test #23: FileIOTests ...................... Passed 0.10 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 5 tests from 1 test case.
24: [----------] Global test environment set-up.
24: [----------] 5 tests from PullTest
24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
24: [----------] 5 tests from PullTest (0 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 5 tests from 1 test case ran. (0 ms total)
24: [ PASSED ] 5 tests.
24/40 Test #24: PullTest ......................... Passed 0.05 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 12 tests from 4 test cases.
25: [----------] Global test environment set-up.
25: [----------] 1 test from BiasTest
25: [ RUN ] BiasTest.DetectsCovering
25: [ OK ] BiasTest.DetectsCovering (5 ms)
25: [----------] 1 test from BiasTest (5 ms total)
25:
25: [----------] 1 test from gridTest
25: [ RUN ] gridTest.neighborhood
25: [ OK ] gridTest.neighborhood (10 ms)
25: [----------] 1 test from gridTest (10 ms total)
25:
25: [----------] 8 tests from WithParameters/BiasTest
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (3 ms)
25: [----------] 8 tests from WithParameters/BiasTest (22 ms total)
25:
25: [----------] 2 tests from WithParameters/BiasStateTest
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (2 ms)
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
25: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 12 tests from 4 test cases ran. (40 ms total)
25: [ PASSED ] 12 tests.
25/40 Test #25: AwhTest .......................... Passed 0.10 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 86 tests from 3 test cases.
26: [----------] Global test environment set-up.
26: [----------] 41 tests from SimdScalarTest
26: [ RUN ] SimdScalarTest.load
26: [ OK ] SimdScalarTest.load (0 ms)
26: [ RUN ] SimdScalarTest.loadU
26: [ OK ] SimdScalarTest.loadU (0 ms)
26: [ RUN ] SimdScalarTest.store
26: [ OK ] SimdScalarTest.store (0 ms)
26: [ RUN ] SimdScalarTest.storeU
26: [ OK ] SimdScalarTest.storeU (0 ms)
26: [ RUN ] SimdScalarTest.setZero
26: [ OK ] SimdScalarTest.setZero (0 ms)
26: [ RUN ] SimdScalarTest.andNot
26: [ OK ] SimdScalarTest.andNot (0 ms)
26: [ RUN ] SimdScalarTest.fma
26: [ OK ] SimdScalarTest.fma (0 ms)
26: [ RUN ] SimdScalarTest.fms
26: [ OK ] SimdScalarTest.fms (0 ms)
26: [ RUN ] SimdScalarTest.fnma
26: [ OK ] SimdScalarTest.fnma (0 ms)
26: [ RUN ] SimdScalarTest.fnms
26: [ OK ] SimdScalarTest.fnms (0 ms)
26: [ RUN ] SimdScalarTest.maskAdd
26: [ OK ] SimdScalarTest.maskAdd (0 ms)
26: [ RUN ] SimdScalarTest.maskzMul
26: [ OK ] SimdScalarTest.maskzMul (0 ms)
26: [ RUN ] SimdScalarTest.maskzFma
26: [ OK ] SimdScalarTest.maskzFma (0 ms)
26: [ RUN ] SimdScalarTest.abs
26: [ OK ] SimdScalarTest.abs (0 ms)
26: [ RUN ] SimdScalarTest.max
26: [ OK ] SimdScalarTest.max (0 ms)
26: [ RUN ] SimdScalarTest.min
26: [ OK ] SimdScalarTest.min (0 ms)
26: [ RUN ] SimdScalarTest.round
26: [ OK ] SimdScalarTest.round (0 ms)
26: [ RUN ] SimdScalarTest.trunc
26: [ OK ] SimdScalarTest.trunc (0 ms)
26: [ RUN ] SimdScalarTest.reduce
26: [ OK ] SimdScalarTest.reduce (0 ms)
26: [ RUN ] SimdScalarTest.testBits
26: [ OK ] SimdScalarTest.testBits (0 ms)
26: [ RUN ] SimdScalarTest.anyTrue
26: [ OK ] SimdScalarTest.anyTrue (0 ms)
26: [ RUN ] SimdScalarTest.selectByMask
26: [ OK ] SimdScalarTest.selectByMask (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMask
26: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
26: [ RUN ] SimdScalarTest.blend
26: [ OK ] SimdScalarTest.blend (0 ms)
26: [ RUN ] SimdScalarTest.cvtR2I
26: [ OK ] SimdScalarTest.cvtR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvttR2I
26: [ OK ] SimdScalarTest.cvttR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvtI2R
26: [ OK ] SimdScalarTest.cvtI2R (0 ms)
26: [ RUN ] SimdScalarTest.cvtF2D
26: [ OK ] SimdScalarTest.cvtF2D (0 ms)
26: [ RUN ] SimdScalarTest.cvtD2D
26: [ OK ] SimdScalarTest.cvtD2D (0 ms)
26: [ RUN ] SimdScalarTest.loadI
26: [ OK ] SimdScalarTest.loadI (0 ms)
26: [ RUN ] SimdScalarTest.loadUI
26: [ OK ] SimdScalarTest.loadUI (0 ms)
26: [ RUN ] SimdScalarTest.storeI
26: [ OK ] SimdScalarTest.storeI (0 ms)
26: [ RUN ] SimdScalarTest.storeUI
26: [ OK ] SimdScalarTest.storeUI (0 ms)
26: [ RUN ] SimdScalarTest.andNotI
26: [ OK ] SimdScalarTest.andNotI (0 ms)
26: [ RUN ] SimdScalarTest.testBitsI
26: [ OK ] SimdScalarTest.testBitsI (0 ms)
26: [ RUN ] SimdScalarTest.selectByMaskI
26: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMaskI
26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
26: [ RUN ] SimdScalarTest.blendI
26: [ OK ] SimdScalarTest.blendI (0 ms)
26: [ RUN ] SimdScalarTest.cvtB2IB
26: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
26: [ RUN ] SimdScalarTest.cvtIB2B
26: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
26: [ RUN ] SimdScalarTest.expandScalarsToTriplets
26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
26: [----------] 41 tests from SimdScalarTest (2 ms total)
26:
26: [----------] 8 tests from SimdScalarUtilTest
26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
26: [----------] 8 tests from SimdScalarUtilTest (0 ms total)
26:
26: [----------] 37 tests from SimdScalarMathTest
26: [ RUN ] SimdScalarMathTest.copysign
26: [ OK ] SimdScalarMathTest.copysign (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPair
26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
26: [ RUN ] SimdScalarMathTest.inv
26: [ OK ] SimdScalarMathTest.inv (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrt
26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
26: [ RUN ] SimdScalarMathTest.log
26: [ OK ] SimdScalarMathTest.log (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2
26: [ OK ] SimdScalarMathTest.exp2 (0 ms)
26: [ RUN ] SimdScalarMathTest.exp
26: [ OK ] SimdScalarMathTest.exp (0 ms)
26: [ RUN ] SimdScalarMathTest.erf
26: [ OK ] SimdScalarMathTest.erf (0 ms)
26: [ RUN ] SimdScalarMathTest.erfc
26: [ OK ] SimdScalarMathTest.erfc (0 ms)
26: [ RUN ] SimdScalarMathTest.sincos
26: [ OK ] SimdScalarMathTest.sincos (0 ms)
26: [ RUN ] SimdScalarMathTest.sin
26: [ OK ] SimdScalarMathTest.sin (1 ms)
26: [ RUN ] SimdScalarMathTest.cos
26: [ OK ] SimdScalarMathTest.cos (0 ms)
26: [ RUN ] SimdScalarMathTest.tan
26: [ OK ] SimdScalarMathTest.tan (0 ms)
26: [ RUN ] SimdScalarMathTest.asin
26: [ OK ] SimdScalarMathTest.asin (0 ms)
26: [ RUN ] SimdScalarMathTest.acos
26: [ OK ] SimdScalarMathTest.acos (0 ms)
26: [ RUN ] SimdScalarMathTest.atan
26: [ OK ] SimdScalarMathTest.atan (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2
26: [ OK ] SimdScalarMathTest.atan2 (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrection
26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.invSingleAccuracy
26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.logSingleAccuracy
26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.expSingleAccuracy
26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
26: [----------] 37 tests from SimdScalarMathTest (2 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 86 tests from 3 test cases ran. (5 ms total)
26: [ PASSED ] 86 tests.
26/40 Test #26: SimdUnitTests .................... Passed 0.08 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 6 tests from 6 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from CompatibilityHelper
27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles
27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms)
27: [----------] 1 test from CompatibilityHelper (0 ms total)
27:
27: [----------] 1 test from NotNullConstruction
27: [ RUN ] NotNullConstruction.Works
27: [ OK ] NotNullConstruction.Works (0 ms)
27: [----------] 1 test from NotNullConstruction (0 ms total)
27:
27: [----------] 1 test from NotNullCasting
27: [ RUN ] NotNullCasting.Works
27: [ OK ] NotNullCasting.Works (0 ms)
27: [----------] 1 test from NotNullCasting (0 ms total)
27:
27: [----------] 1 test from NotNullAssignment
27: [ RUN ] NotNullAssignment.Works
27: [ OK ] NotNullAssignment.Works (0 ms)
27: [----------] 1 test from NotNullAssignment (0 ms total)
27:
27: [----------] 1 test from MakeNotNull
27: [ RUN ] MakeNotNull.Works
27: [ OK ] MakeNotNull.Works (0 ms)
27: [----------] 1 test from MakeNotNull (0 ms total)
27:
27: [----------] 1 test from NotNull
27: [ RUN ] NotNull.WorksInContainers
27: [ OK ] NotNull.WorksInContainers (0 ms)
27: [----------] 1 test from NotNull (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 6 tests from 6 test cases ran. (1 ms total)
27: [ PASSED ] 6 tests.
27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.05 sec
test 28
Start 28: GmxAnaTest
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
28: Test timeout computed to be: 600
28: [==========] Running 26 tests from 5 test cases.
28: [----------] Global test environment set-up.
28: [----------] 5 tests from Entropy
28: [ RUN ] Entropy.Schlitter_300_NoLinear
28: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms)
28: [ RUN ] Entropy.Schlitter_300_Linear
28: [ OK ] Entropy.Schlitter_300_Linear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
28: [ RUN ] Entropy.QuasiHarmonic_200_Linear
28: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
28: [----------] 5 tests from Entropy (1 ms total)
28:
28: [----------] 3 tests from MsdTest
28: [ RUN ] MsdTest.threeDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.threeDimensionalDiffusion (7 ms)
28: [ RUN ] MsdTest.twoDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.twoDimensionalDiffusion (4 ms)
28: [ RUN ] MsdTest.oneDimensionalDiffusion
28:
28: Select a group to calculate mean squared displacement for:
28: Group 0 ( particles) has 3 elements
28: There is one group in the index
28:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
28:
28: Used 1 restart points spaced 200 ps over 9 ps
28:
28: Fitting from 1 to 8 ps
28:
28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
28: [ OK ] MsdTest.oneDimensionalDiffusion (4 ms)
28: [----------] 3 tests from MsdTest (16 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: trr version: GMX_trn_file (single precision)
28:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (9 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
28: Group 0 ( System) has 6 elements
28: Group 1 ( Water) has 6 elements
28: Group 2 ( SOL) has 6 elements
28: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
28: Selected 0: 'System'
28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (9 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (54 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (23 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (22 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (22 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (28 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm)
28: -> frame 0 time 0.000
't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (29 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
28: Will write tng: Trajectory file (tng format)
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (29 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (153 ms total)
28:
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from gro file '', 6 atoms.
28:
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm)
28: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
28: Precision of /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm)
28: -> frame 0 time 0.000
't= 0.00000', 6 atoms
28:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (5 ms)
28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
28: Will write trr: Trajectory in portable xdr format
28: Group 0 ( System) has 6 elements
28: Group 1 (FirstWaterMolecule) has 3 elements
28: Group 2 (SecondWaterMolecule) has 3 elements
28: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
28:
28: Note that major changes are planned in future for trjconv, to improve usability and utility.
28: Select group for output
28: Selected 2: 'SecondWaterMolecule'
28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (5 ms)
28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (30 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 26 tests from 5 test cases ran. (257 ms total)
28: [ PASSED ] 26 tests.
28/40 Test #28: GmxAnaTest ....................... Passed 0.31 sec
test 29
Start 29: GmxPreprocessTests
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
29: Test timeout computed to be: 30
29: [==========] Running 26 tests from 4 test cases.
29: [----------] Global test environment set-up.
29: [----------] 4 tests from GenconfTest
29: [ RUN ] GenconfTest.nbox_Works
29: [ OK ] GenconfTest.nbox_Works (5 ms)
29: [ RUN ] GenconfTest.nbox_norenumber_Works
29: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms)
29: [ RUN ] GenconfTest.nbox_dist_Works
29: [ OK ] GenconfTest.nbox_dist_Works (5 ms)
29: [ RUN ] GenconfTest.nbox_rot_Works
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: center of geometry: 1.733667, 1.477000, 0.905167
29: [ OK ] GenconfTest.nbox_rot_Works (4 ms)
29: [----------] 4 tests from GenconfTest (18 ms total)
29:
29: [----------] 5 tests from InsertMoleculesTest
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 8 atoms)!
29:
29: Added 1 molecules (out of 1 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
29:
29: Output configuration contains 8 atoms in 4 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (10 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 2 atoms)!
29:
Try 2 success (now 4 atoms)!
29:
Try 3 success (now 6 atoms)!
29:
Try 4 success (now 8 atoms)!
29:
Try 5 success (now 10 atoms)!
29:
29: Added 5 molecules (out of 5 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
29:
29: Output configuration contains 10 atoms in 10 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (9 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 8 atoms)!
29:
Try 2 success (now 10 atoms)!
29:
29: Added 2 molecules (out of 2 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
29:
29: Output configuration contains 10 atoms in 4 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (10 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
29: Reading solute configuration
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29:
Try 1 success (now 650 atoms)!
29:
Try 2 success (now 652 atoms)!
29:
Try 3 success (now 654 atoms)!
29:
Try 4 success (now 656 atoms)!
29:
29: Added 4 molecules (out of 4 requested)
29: Replaced 8 residues (24 atoms)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
29:
29: Output configuration contains 632 atoms in 212 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (44 ms)
29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Using random seed 1997
29: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
29:
29:
Try 1 success (now 2 atoms)!
29:
Try 2 success (now 4 atoms)!
29:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
29:
Try 13 success (now 6 atoms)!
29:
29: Added 3 molecules (out of 4 requested)
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
29:
29: Output configuration contains 6 atoms in 3 residues
29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (10 ms)
29: [----------] 5 tests from InsertMoleculesTest (83 ms total)
29:
29: [----------] 12 tests from GetIrTest
29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: Ignoring obsolete mdp entry 'title'
29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (14 ms)
29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme
29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (14 ms)
29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (14 ms)
29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (14 ms)
29: [ RUN ] GetIrTest.EmptyInputWorks
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.EmptyInputWorks (14 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricField
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricField (14 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (14 ms)
29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (14 ms)
29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys
29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (10 ms)
29: [ RUN ] GetIrTest.ImplicitSolventNoWorks
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.ImplicitSolventNoWorks (14 ms)
29: [ RUN ] GetIrTest.ImplicitSolventYesWorks
29: [ OK ] GetIrTest.ImplicitSolventYesWorks (23 ms)
29: [ RUN ] GetIrTest.HandlesMimic
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]:
29: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
29: scheme was introduced, but the group scheme was still the default. The
29: default is now the Verlet scheme, so you will observe different behaviour.
29:
29: [ OK ] GetIrTest.HandlesMimic (15 ms)
29: [----------] 12 tests from GetIrTest (176 ms total)
29:
29: [----------] 5 tests from SolvateTest
29: [ RUN ] SolvateTest.cs_box_Works
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 1x1x1 boxes
29: Solvent box contains 270 atoms in 90 residues
29: Removed 129 solvent atoms due to solvent-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 47 residues
29: Generated solvent containing 141 atoms in 47 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
29:
29: Output configuration contains 141 atoms in 47 residues
29: Volume : 1.331 (nm^3)
29: Density : 1056.36 (g/l)
29: Number of solvent molecules: 47
29:
29: [ OK ] SolvateTest.cs_box_Works (51 ms)
29: [ RUN ] SolvateTest.cs_cp_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 886 residues
29: Generated solvent containing 2658 atoms in 886 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
29:
29: Output configuration contains 2664 atoms in 888 residues
29: Volume : 27.2709 (nm^3)
29: Density : 974.776 (g/l)
29: Number of solvent molecules: 886
29:
29: [ OK ] SolvateTest.cs_cp_Works (245 ms)
29: [ RUN ] SolvateTest.cs_cp_p_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 886 residues
29: Generated solvent containing 2658 atoms in 886 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
29:
29: Output configuration contains 2664 atoms in 888 residues
29: Volume : 27.2709 (nm^3)
29: Density : 974.776 (g/l)
29: Number of solvent molecules: 886
29:
29: Processing topology
29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top)
29: [ OK ] SolvateTest.cs_cp_p_Works (217 ms)
29: [ RUN ] SolvateTest.shell_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 2x2x2 boxes
29: Solvent box contains 3660 atoms in 1220 residues
29: Removed 987 solvent atoms due to solvent-solvent overlap
29: Removed 1902 solvent atoms more than 1.000000 nm from solute.
29: Removed 15 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 1 molecule type:
29: SOL ( 3 atoms): 252 residues
29: Generated solvent containing 756 atoms in 252 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
29:
29: Output configuration contains 762 atoms in 254 residues
29: Volume : 27.2709 (nm^3)
29: Density : 279.3 (g/l)
29: Number of solvent molecules: 252
29:
29: [ OK ] SolvateTest.shell_Works (119 ms)
29: [ RUN ] SolvateTest.update_Topology_Works
29: Reading solute configuration
29: Reading solvent configuration
29:
29: Initialising inter-atomic distances...
29:
29: WARNING: Masses and atomic (Van der Waals) radii will be guessed
29: based on residue and atom names, since they could not be
29: definitively assigned from the information in your input
29: files. These guessed numbers might deviate from the mass
29: and radius of the atom type. Please check the output
29: files if necessary.
29:
29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
29: from the source below. This means the results may be different
29: compared to previous GROMACS versions.
29:
29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
29: A. Bondi
29: van der Waals Volumes and Radii
29: J. Phys. Chem. 68 (1964) pp. 441-451
29: -------- -------- --- Thank You --- -------- --------
29:
29: Generating solvent configuration
29: Will generate new solvent configuration of 3x3x3 boxes
29: Solvent box contains 14952 atoms in 4984 residues
29: Removed 2787 solvent atoms due to solvent-solvent overlap
29: Removed 30 solvent atoms due to solute-solvent overlap
29: Sorting configuration
29: Found 2 different molecule types:
29: HOH ( 3 atoms): 1876 residues
29: SOL ( 3 atoms): 2169 residues
29: Generated solvent containing 0 atoms in 0 residues
29: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
29:
29: Output configuration contains 12141 atoms in 4047 residues
29: Volume : 125 (nm^3)
29: Density : 968.963 (g/l)
29: Number of solvent molecules: 4045
29:
29: Processing topology
29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
29: [ OK ] SolvateTest.update_Topology_Works (770 ms)
29: [----------] 5 tests from SolvateTest (1403 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 26 tests from 4 test cases ran. (1680 ms total)
29: [ PASSED ] 26 tests.
29/40 Test #29: GmxPreprocessTests ............... Passed 1.74 sec
test 30
Start 30: Pdb2gmxTest
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmxTest.xml"
30: Test timeout computed to be: 480
30: [==========] Running 80 tests from 6 test cases.
30: [----------] Global test environment set-up.
30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (2085 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (2196 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (2065 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (1892 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (2007 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
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Atomtype 171
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Atomtype 180
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Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
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Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
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Atomtype 673
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Atomtype 676
Atomtype 677
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Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
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Atomtype 686
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Atomtype 688
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Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
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Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (2222 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (2101 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (1855 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (1764 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
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Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
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Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
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Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
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Atomtype 192
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Atomtype 196
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Atomtype 201
Atomtype 202
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Atomtype 228
Atomtype 229
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Atomtype 232
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Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
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Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
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Atomtype 255
Atomtype 256
Atomtype 257
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Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
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Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
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Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
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Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
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Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
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Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
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Atomtype 331
Atomtype 332
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Atomtype 337
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Atomtype 342
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Atomtype 366
Atomtype 367
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Atomtype 371
Atomtype 372
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Atomtype 377
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Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
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Atomtype 390
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Atomtype 404
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Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
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Atomtype 436
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Atomtype 440
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Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
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Atomtype 459
Atomtype 460
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Atomtype 471
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Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
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Atomtype 511
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Atomtype 514
Atomtype 515
Atomtype 516
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Atomtype 520
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Atomtype 522
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Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
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Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
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Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
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Atomtype 665
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Atomtype 680
Atomtype 681
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Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
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Atomtype 708
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Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
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Atomtype 720
Atomtype 721
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Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
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Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (2084 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (1874 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (1716 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (2012 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (2216 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
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Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
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Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
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Atomtype 672
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Atomtype 680
Atomtype 681
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Atomtype 691
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Atomtype 693
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Atomtype 695
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Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
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Atomtype 717
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Atomtype 719
Atomtype 720
Atomtype 721
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Atomtype 727
Atomtype 728
Atomtype 729
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Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (1972 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip4p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (1731 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (1792 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (2088 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
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Atomtype 238
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Atomtype 251
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Atomtype 570
Atomtype 571
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Atomtype 634
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Atomtype 636
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Atomtype 640
Atomtype 641
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Atomtype 646
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Atomtype 750
Atomtype 751
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Atomtype 755
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Atomtype 781
Atomtype 782
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Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
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Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (1843 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
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Atomtype 65
Atomtype 66
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Atomtype 68
Atomtype 69
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Atomtype 128
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Atomtype 131
Atomtype 132
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Atomtype 134
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Atomtype 136
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Atomtype 139
Atomtype 140
Atomtype 141
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Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
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Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
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Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
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Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
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Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
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Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
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Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
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Atomtype 283
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Atomtype 285
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Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (1687 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 663 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.112 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (1957 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 778 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.357 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (2144 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 696 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.128 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (1919 ms)
30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
Atomtype 214
Atomtype 215
Atomtype 216
Atomtype 217
Atomtype 218
Atomtype 219
Atomtype 220
Atomtype 221
Atomtype 222
Atomtype 223
Atomtype 224
Atomtype 225
Atomtype 226
Atomtype 227
Atomtype 228
Atomtype 229
Atomtype 230
Atomtype 231
Atomtype 232
Atomtype 233
Atomtype 234
Atomtype 235
Atomtype 236
Atomtype 237
Atomtype 238
Atomtype 239
Atomtype 240
Atomtype 241
Atomtype 242
Atomtype 243
Atomtype 244
Atomtype 245
Atomtype 246
Atomtype 247
Atomtype 248
Atomtype 249
Atomtype 250
Atomtype 251
Atomtype 252
Atomtype 253
Atomtype 254
Atomtype 255
Atomtype 256
Atomtype 257
Atomtype 258
Atomtype 259
Atomtype 260
Atomtype 261
Atomtype 262
Atomtype 263
Atomtype 264
Atomtype 265
Atomtype 266
Atomtype 267
Atomtype 268
Atomtype 269
Atomtype 270
Atomtype 271
Atomtype 272
Atomtype 273
Atomtype 274
Atomtype 275
Atomtype 276
Atomtype 277
Atomtype 278
Atomtype 279
Atomtype 280
Atomtype 281
Atomtype 282
Atomtype 283
Atomtype 284
Atomtype 285
Atomtype 286
Atomtype 287
Atomtype 288
Atomtype 289
Atomtype 290
Atomtype 291
Atomtype 292
Atomtype 293
Atomtype 294
Atomtype 295
Atomtype 296
Atomtype 297
Atomtype 298
Atomtype 299
Atomtype 300
Atomtype 301
Atomtype 302
Atomtype 303
Atomtype 304
Atomtype 305
Atomtype 306
Atomtype 307
Atomtype 308
Atomtype 309
Atomtype 310
Atomtype 311
Atomtype 312
Atomtype 313
Atomtype 314
Atomtype 315
Atomtype 316
Atomtype 317
Atomtype 318
Atomtype 319
Atomtype 320
Atomtype 321
Atomtype 322
Atomtype 323
Atomtype 324
Atomtype 325
Atomtype 326
Atomtype 327
Atomtype 328
Atomtype 329
Atomtype 330
Atomtype 331
Atomtype 332
Atomtype 333
Atomtype 334
Atomtype 335
Atomtype 336
Atomtype 337
Atomtype 338
Atomtype 339
Atomtype 340
Atomtype 341
Atomtype 342
Atomtype 343
Atomtype 344
Atomtype 345
Atomtype 346
Atomtype 347
Atomtype 348
Atomtype 349
Atomtype 350
Atomtype 351
Atomtype 352
Atomtype 353
Atomtype 354
Atomtype 355
Atomtype 356
Atomtype 357
Atomtype 358
Atomtype 359
Atomtype 360
Atomtype 361
Atomtype 362
Atomtype 363
Atomtype 364
Atomtype 365
Atomtype 366
Atomtype 367
Atomtype 368
Atomtype 369
Atomtype 370
Atomtype 371
Atomtype 372
Atomtype 373
Atomtype 374
Atomtype 375
Atomtype 376
Atomtype 377
Atomtype 378
Atomtype 379
Atomtype 380
Atomtype 381
Atomtype 382
Atomtype 383
Atomtype 384
Atomtype 385
Atomtype 386
Atomtype 387
Atomtype 388
Atomtype 389
Atomtype 390
Atomtype 391
Atomtype 392
Atomtype 393
Atomtype 394
Atomtype 395
Atomtype 396
Atomtype 397
Atomtype 398
Atomtype 399
Atomtype 400
Atomtype 401
Atomtype 402
Atomtype 403
Atomtype 404
Atomtype 405
Atomtype 406
Atomtype 407
Atomtype 408
Atomtype 409
Atomtype 410
Atomtype 411
Atomtype 412
Atomtype 413
Atomtype 414
Atomtype 415
Atomtype 416
Atomtype 417
Atomtype 418
Atomtype 419
Atomtype 420
Atomtype 421
Atomtype 422
Atomtype 423
Atomtype 424
Atomtype 425
Atomtype 426
Atomtype 427
Atomtype 428
Atomtype 429
Atomtype 430
Atomtype 431
Atomtype 432
Atomtype 433
Atomtype 434
Atomtype 435
Atomtype 436
Atomtype 437
Atomtype 438
Atomtype 439
Atomtype 440
Atomtype 441
Atomtype 442
Atomtype 443
Atomtype 444
Atomtype 445
Atomtype 446
Atomtype 447
Atomtype 448
Atomtype 449
Atomtype 450
Atomtype 451
Atomtype 452
Atomtype 453
Atomtype 454
Atomtype 455
Atomtype 456
Atomtype 457
Atomtype 458
Atomtype 459
Atomtype 460
Atomtype 461
Atomtype 462
Atomtype 463
Atomtype 464
Atomtype 465
Atomtype 466
Atomtype 467
Atomtype 468
Atomtype 469
Atomtype 470
Atomtype 471
Atomtype 472
Atomtype 473
Atomtype 474
Atomtype 475
Atomtype 476
Atomtype 477
Atomtype 478
Atomtype 479
Atomtype 480
Atomtype 481
Atomtype 482
Atomtype 483
Atomtype 484
Atomtype 485
Atomtype 486
Atomtype 487
Atomtype 488
Atomtype 489
Atomtype 490
Atomtype 491
Atomtype 492
Atomtype 493
Atomtype 494
Atomtype 495
Atomtype 496
Atomtype 497
Atomtype 498
Atomtype 499
Atomtype 500
Atomtype 501
Atomtype 502
Atomtype 503
Atomtype 504
Atomtype 505
Atomtype 506
Atomtype 507
Atomtype 508
Atomtype 509
Atomtype 510
Atomtype 511
Atomtype 512
Atomtype 513
Atomtype 514
Atomtype 515
Atomtype 516
Atomtype 517
Atomtype 518
Atomtype 519
Atomtype 520
Atomtype 521
Atomtype 522
Atomtype 523
Atomtype 524
Atomtype 525
Atomtype 526
Atomtype 527
Atomtype 528
Atomtype 529
Atomtype 530
Atomtype 531
Atomtype 532
Atomtype 533
Atomtype 534
Atomtype 535
Atomtype 536
Atomtype 537
Atomtype 538
Atomtype 539
Atomtype 540
Atomtype 541
Atomtype 542
Atomtype 543
Atomtype 544
Atomtype 545
Atomtype 546
Atomtype 547
Atomtype 548
Atomtype 549
Atomtype 550
Atomtype 551
Atomtype 552
Atomtype 553
Atomtype 554
Atomtype 555
Atomtype 556
Atomtype 557
Atomtype 558
Atomtype 559
Atomtype 560
Atomtype 561
Atomtype 562
Atomtype 563
Atomtype 564
Atomtype 565
Atomtype 566
Atomtype 567
Atomtype 568
Atomtype 569
Atomtype 570
Atomtype 571
Atomtype 572
Atomtype 573
Atomtype 574
Atomtype 575
Atomtype 576
Atomtype 577
Atomtype 578
Atomtype 579
Atomtype 580
Atomtype 581
Atomtype 582
Atomtype 583
Atomtype 584
Atomtype 585
Atomtype 586
Atomtype 587
Atomtype 588
Atomtype 589
Atomtype 590
Atomtype 591
Atomtype 592
Atomtype 593
Atomtype 594
Atomtype 595
Atomtype 596
Atomtype 597
Atomtype 598
Atomtype 599
Atomtype 600
Atomtype 601
Atomtype 602
Atomtype 603
Atomtype 604
Atomtype 605
Atomtype 606
Atomtype 607
Atomtype 608
Atomtype 609
Atomtype 610
Atomtype 611
Atomtype 612
Atomtype 613
Atomtype 614
Atomtype 615
Atomtype 616
Atomtype 617
Atomtype 618
Atomtype 619
Atomtype 620
Atomtype 621
Atomtype 622
Atomtype 623
Atomtype 624
Atomtype 625
Atomtype 626
Atomtype 627
Atomtype 628
Atomtype 629
Atomtype 630
Atomtype 631
Atomtype 632
Atomtype 633
Atomtype 634
Atomtype 635
Atomtype 636
Atomtype 637
Atomtype 638
Atomtype 639
Atomtype 640
Atomtype 641
Atomtype 642
Atomtype 643
Atomtype 644
Atomtype 645
Atomtype 646
Atomtype 647
Atomtype 648
Atomtype 649
Atomtype 650
Atomtype 651
Atomtype 652
Atomtype 653
Atomtype 654
Atomtype 655
Atomtype 656
Atomtype 657
Atomtype 658
Atomtype 659
Atomtype 660
Atomtype 661
Atomtype 662
Atomtype 663
Atomtype 664
Atomtype 665
Atomtype 666
Atomtype 667
Atomtype 668
Atomtype 669
Atomtype 670
Atomtype 671
Atomtype 672
Atomtype 673
Atomtype 674
Atomtype 675
Atomtype 676
Atomtype 677
Atomtype 678
Atomtype 679
Atomtype 680
Atomtype 681
Atomtype 682
Atomtype 683
Atomtype 684
Atomtype 685
Atomtype 686
Atomtype 687
Atomtype 688
Atomtype 689
Atomtype 690
Atomtype 691
Atomtype 692
Atomtype 693
Atomtype 694
Atomtype 695
Atomtype 696
Atomtype 697
Atomtype 698
Atomtype 699
Atomtype 700
Atomtype 701
Atomtype 702
Atomtype 703
Atomtype 704
Atomtype 705
Atomtype 706
Atomtype 707
Atomtype 708
Atomtype 709
Atomtype 710
Atomtype 711
Atomtype 712
Atomtype 713
Atomtype 714
Atomtype 715
Atomtype 716
Atomtype 717
Atomtype 718
Atomtype 719
Atomtype 720
Atomtype 721
Atomtype 722
Atomtype 723
Atomtype 724
Atomtype 725
Atomtype 726
Atomtype 727
Atomtype 728
Atomtype 729
Atomtype 730
Atomtype 731
Atomtype 732
Atomtype 733
Atomtype 734
Atomtype 735
Atomtype 736
Atomtype 737
Atomtype 738
Atomtype 739
Atomtype 740
Atomtype 741
Atomtype 742
Atomtype 743
Atomtype 744
Atomtype 745
Atomtype 746
Atomtype 747
Atomtype 748
Atomtype 749
Atomtype 750
Atomtype 751
Atomtype 752
Atomtype 753
Atomtype 754
Atomtype 755
Atomtype 756
Atomtype 757
Atomtype 758
Atomtype 759
Atomtype 760
Atomtype 761
Atomtype 762
Atomtype 763
Atomtype 764
Atomtype 765
Atomtype 766
Atomtype 767
Atomtype 768
Atomtype 769
Atomtype 770
Atomtype 771
Atomtype 772
Atomtype 773
Atomtype 774
Atomtype 775
Atomtype 776
Atomtype 777
Atomtype 778
Atomtype 779
Atomtype 780
Atomtype 781
Atomtype 782
Atomtype 783
Atomtype 784
Atomtype 785
Atomtype 786
Atomtype 787
Atomtype 788
Atomtype 789
Atomtype 790
Atomtype 791
Atomtype 792
Atomtype 793
Atomtype 794
Atomtype 795
Atomtype 796
Atomtype 797
Atomtype 798
Atomtype 799
Atomtype 800
Atomtype 801
Atomtype 802
Atomtype 803
Atomtype 804
Atomtype 805
Atomtype 806
Atomtype 807
Atomtype 808
Atomtype 809
Atomtype 810
Atomtype 811
Atomtype 812
Atomtype 813
Atomtype 814
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 618 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.883 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Oplsaa force field in directory oplsaa.ff
30:
30: going to rename oplsaa.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Oplsaa)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: PRO-COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Oplsaa force field and the tip5p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (1911 ms)
30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (47139 ms total)
30:
30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (963 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (982 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (902 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (794 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Marked 37 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 37 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (869 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Marked 53 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 51 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (1069 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Marked 36 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 36 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (926 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Marked 33 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 31 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (817 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (838 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (994 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (811 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (794 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 172, now 167
30: Marked 37 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 305 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 77 impropers, 241 angles
30: 267 pairs, 167 bonds and 37 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 165 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (900 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 216, now 211
30: Marked 53 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 429 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 134 impropers, 316 angles
30: 273 pairs, 211 bonds and 51 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 202 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (1109 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 179, now 174
30: Marked 36 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 349 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 102 impropers, 260 angles
30: 242 pairs, 174 bonds and 36 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 168 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (926 ms)
30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 159, now 154
30: Marked 33 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 299 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 80 impropers, 227 angles
30: 232 pairs, 154 bonds and 31 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos43a1 force field in directory gromos43a1.ff
30:
30: going to rename gromos43a1.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos43a1)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 150 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos43a1 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (765 ms)
30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (14468 ms total)
30:
30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (851 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (1079 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (877 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (776 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Marked 39 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 39 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (999 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Marked 57 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 55 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (1086 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Marked 38 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 38 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (902 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Marked 35 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 33 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spc water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (866 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 0 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (881 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (1026 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 0 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (899 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 0 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (805 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Making bonds...
30: Number of bonds was 174, now 169
30: Marked 39 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 267 pairs
30: Before cleaning: 312 dihedrals
30: Making cmap torsions...
30: There are 90 dihedrals, 79 impropers, 245 angles
30: 267 pairs, 169 bonds and 39 virtual sites
30: Total mass 1846.116 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 167 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (871 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Making bonds...
30: Number of bonds was 220, now 215
30: Marked 57 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 273 pairs
30: Before cleaning: 443 dihedrals
30: Making cmap torsions...
30: There are 93 dihedrals, 138 impropers, 324 angles
30: 273 pairs, 215 bonds and 55 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 206 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (1079 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Making bonds...
30: Number of bonds was 181, now 176
30: Marked 38 virtual sites
30: Added 4 dummy masses
30: Added 8 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 242 pairs
30: Before cleaning: 356 dihedrals
30: Making cmap torsions...
30: There are 81 dihedrals, 104 impropers, 264 angles
30: 242 pairs, 176 bonds and 38 virtual sites
30: Total mass 1861.132 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 170 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (966 ms)
30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
30: Using default: not generating all possible dihedrals
30: Using default: excluding 3 bonded neighbors
30: Using default: generating 1,4 H--H interactions
30: Using default: removing proper dihedrals found on the same bond as a proper dihedral
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Making bonds...
30: Number of bonds was 161, now 156
30: Marked 35 virtual sites
30: Added 4 dummy masses
30: Added 10 new constraints
30: Generating angles, dihedrals and pairs...
30:
30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom H used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30:
30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
30: to an entry in the topology database, but the atom O used in
30: an interaction of type angle in that entry is not found in the
30: input file. Perhaps your atom and/or residue naming needs to be
30: fixed.
30:
30:
30: Before cleaning: 232 pairs
30: Before cleaning: 306 dihedrals
30: Making cmap torsions...
30: There are 78 dihedrals, 82 impropers, 231 angles
30: 232 pairs, 156 bonds and 33 virtual sites
30: Total mass 1662.887 a.m.u.
30: Total charge -0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Gromos53a6 force field in directory gromos53a6.ff
30:
30: going to rename gromos53a6.ff/aminoacids.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Gromos53a6)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 152 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Gromos53a6 force field and the spce water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (828 ms)
30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (14791 ms total)
30:
30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 255, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 691 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 691 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.132 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (1608 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 291, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 788 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 788 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.366 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (1830 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 262, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 727 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 727 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.124 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (1736 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 233, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 634 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 634 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.888 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (1438 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 255, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 691 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 691 dihedrals, 51 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.132 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (1793 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 291, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 788 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 788 dihedrals, 72 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.366 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (1967 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 262, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 727 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 727 dihedrals, 56 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.124 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (1764 ms)
30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
30:
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
30:
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
30: Making bonds...
30: Number of bonds was 233, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 634 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 634 dihedrals, 48 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.888 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
30:
30: going to rename amber99sb-ildn.ff/aminoacids.r2b
30: going to rename amber99sb-ildn.ff/dna.r2b
30: going to rename amber99sb-ildn.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Amber99sb-ildn)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Amber99sb-ildn force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (1671 ms)
30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (13808 ms total)
30:
30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 254, now 254
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 663 dihedrals, 48 impropers, 457 angles
30: 650 pairs, 254 bonds and 0 virtual sites
30: Total mass 1846.115 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (1567 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 290, now 290
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 778 dihedrals, 49 impropers, 516 angles
30: 736 pairs, 290 bonds and 0 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (1804 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 261, now 261
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 696 dihedrals, 39 impropers, 472 angles
30: 667 pairs, 261 bonds and 0 virtual sites
30: Total mass 1861.130 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (1568 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 232, now 232
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 618 dihedrals, 38 impropers, 419 angles
30: 597 pairs, 232 bonds and 0 virtual sites
30: Total mass 1662.885 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (1361 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 254, now 254
30: Marked 124 virtual sites
30: Added 16 dummy masses
30: Added 26 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 653 pairs
30: Before cleaning: 663 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 663 dihedrals, 48 impropers, 457 angles
30: 650 pairs, 254 bonds and 130 virtual sites
30: Total mass 1846.115 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 128
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (128 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 252 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (1693 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 30 donors and 22 acceptors were found.
30: There are 36 hydrogen bonds
30: Will use HISE for residue 29
30: Will use HISE for residue 32
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS27 HIS29
30: SG90 NE2111
30: HIS29 NE2111 0.987
30: HIS32 NE2135 1.590 1.155
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 290, now 290
30: Marked 132 virtual sites
30: Added 10 dummy masses
30: Added 19 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 748 pairs
30: Before cleaning: 778 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 778 dihedrals, 49 impropers, 516 angles
30: 736 pairs, 290 bonds and 133 virtual sites
30: Total mass 2088.361 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 149
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (149 atoms, 16 residues)
30: Identified residue THR18 as a starting terminus.
30: Identified residue PHE33 as a ending terminus.
30: Start terminus THR-18: NH3+
30: End terminus PHE-33: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 281 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (1941 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 22 acceptors were found.
30: There are 26 hydrogen bonds
30: Will use HISE for residue 45
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS45
30: NE295
30: MET46 SD102 1.078
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 261, now 261
30: Marked 123 virtual sites
30: Added 22 dummy masses
30: Added 35 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 676 pairs
30: Before cleaning: 696 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 696 dihedrals, 39 impropers, 472 angles
30: 667 pairs, 261 bonds and 132 virtual sites
30: Total mass 1861.130 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 132
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (132 atoms, 16 residues)
30: Identified residue ALA34 as a starting terminus.
30: Identified residue ALA49 as a ending terminus.
30: Start terminus ALA-34: NH3+
30: End terminus ALA-49: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (1857 ms)
30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 22 donors and 21 acceptors were found.
30: There are 30 hydrogen bonds
30: Will use HISE for residue 60
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS60
30: NE285
30: CYS62 SG98 0.803
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 232, now 232
30: Marked 111 virtual sites
30: Added 18 dummy masses
30: Added 31 new constraints
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 603 pairs
30: Before cleaning: 618 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 14 cmap torsion pairs
30: There are 618 dihedrals, 38 impropers, 419 angles
30: 597 pairs, 232 bonds and 116 virtual sites
30: Total mass 1662.885 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
30:
30: chain #res #atoms
30: 1 ' ' 16 117
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 (117 atoms, 16 residues)
30: Identified residue LYS50 as a starting terminus.
30: Identified residue PRO65 as a ending terminus.
30: Start terminus LYS-50: NH3+
30: End terminus PRO-65: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 228 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (1595 ms)
30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (13386 ms total)
30:
30: [----------] 8 tests from ChainSep/Pdb2gmxTest
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 258, now 258
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 651 pairs
30: Before cleaning: 661 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 10 cmap torsion pairs
30: There are 661 dihedrals, 46 impropers, 463 angles
30: 648 pairs, 258 bonds and 0 virtual sites
30: Total mass 1882.146 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on changing chain id only (ignoring TER records).
30:
30: Merged chains into joint molecule definitions at 2 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Identified residue PHE6 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Start terminus PHE-6: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 258 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (1577 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 50, now 50
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 123 pairs
30: Before cleaning: 123 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 123 dihedrals, 9 impropers, 88 angles
30: 123 pairs, 50 bonds and 0 virtual sites
30: Total mass 434.421 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 10 donors and 7 acceptors were found.
30: There are 7 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: HIS8
30: NE223
30: MET12 SD55 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 125, now 125
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 317 pairs
30: Before cleaning: 322 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 5 cmap torsion pairs
30: There are 322 dihedrals, 19 impropers, 227 angles
30: 314 pairs, 125 bonds and 0 virtual sites
30: Total mass 846.083 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 258 atoms and 16 residues
30: Total mass in system 1882.146 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on changing chain id only (ignoring TER records).
30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 4 28
30: 2 'B' 7 58
30: 3 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (28 atoms, 4 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 51 atoms
30: Chain time...
30: Processing chain 2 'B' (58 atoms, 7 residues)
30: Identified residue PHE6 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus PHE-6: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 7 residues with 124 atoms
30: Chain time...
30: Processing chain 3 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 51 atoms 4 residues
30: Including chain 2 in system: 124 atoms 7 residues
30: Including chain 3 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (291 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 258, now 258
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 651 pairs
30: Before cleaning: 661 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 10 cmap torsion pairs
30: There are 661 dihedrals, 46 impropers, 463 angles
30: 648 pairs, 258 bonds and 0 virtual sites
30: Total mass 1882.146 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records only (ignoring chain id).
30:
30: Merged chains into joint molecule definitions at 2 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus ILE-9: COO-
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 258 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (1595 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 10 donors and 12 acceptors were found.
30: There are 13 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3
30: SG9
30: HIS8 NE251 1.055
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 115, now 115
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 288 pairs
30: Before cleaning: 293 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 6 cmap torsion pairs
30: There are 293 dihedrals, 23 impropers, 203 angles
30: 285 pairs, 115 bonds and 0 virtual sites
30: Total mass 888.952 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 60, now 60
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 152 pairs
30: Before cleaning: 152 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 1 cmap torsion pairs
30: There are 152 dihedrals, 5 impropers, 112 angles
30: 152 pairs, 60 bonds and 0 virtual sites
30: Total mass 391.552 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 258 atoms and 16 residues
30: Total mass in system 1882.146 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records only (ignoring chain id).
30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 8 61
30: 2 'B' 3 25
30: 3 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (61 atoms, 8 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus ILE-9: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 8 residues with 114 atoms
30: Chain time...
30: Processing chain 2 'B' (25 atoms, 3 residues)
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 3 residues with 61 atoms
30: Chain time...
30: Processing chain 3 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 114 atoms 8 residues
30: Including chain 2 in system: 61 atoms 3 residues
30: Including chain 3 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (240 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 260, now 260
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 650 pairs
30: Before cleaning: 660 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 8 cmap torsion pairs
30: There are 660 dihedrals, 45 impropers, 466 angles
30: 647 pairs, 260 bonds and 0 virtual sites
30: Total mass 1900.162 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30:
30: Merged chains into joint molecule definitions at 3 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Identified residue PHE6 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Start terminus PHE-6: NH3+
30: End terminus ILE-9: COO-
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 261 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (1541 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 50, now 50
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 123 pairs
30: Before cleaning: 123 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 123 dihedrals, 9 impropers, 88 angles
30: 123 pairs, 50 bonds and 0 virtual sites
30: Total mass 434.421 a.m.u.
30: Total charge -2.000 e
30: Writing topology
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 6 donors and 4 acceptors were found.
30: There are 3 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 67, now 67
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 164 pairs
30: Before cleaning: 169 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 2 cmap torsion pairs
30: There are 169 dihedrals, 13 impropers, 118 angles
30: 161 pairs, 67 bonds and 0 virtual sites
30: Total mass 472.547 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 60, now 60
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 152 pairs
30: Before cleaning: 152 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 1 cmap torsion pairs
30: There are 152 dihedrals, 5 impropers, 112 angles
30: 152 pairs, 60 bonds and 0 virtual sites
30: Total mass 391.552 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 261 atoms and 16 residues
30: Total mass in system 1900.162 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records or chain id changing.
30: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
30: They will be treated as separate chains unless you reorder your file.
30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 4 28
30: 2 'B' 4 33
30: 3 'B' 3 25
30: 4 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (28 atoms, 4 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue GLU5 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus GLU-5: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 51 atoms
30: Chain time...
30: Processing chain 2 'B' (33 atoms, 4 residues)
30: Identified residue PHE6 as a starting terminus.
30: Identified residue ILE9 as a ending terminus.
30: Start terminus PHE-6: NH3+
30: End terminus ILE-9: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 4 residues with 66 atoms
30: Chain time...
30: Processing chain 3 'B' (25 atoms, 3 residues)
30: Identified residue LYS10 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus LYS-10: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 3 residues with 61 atoms
30: Chain time...
30: Processing chain 4 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 51 atoms 4 residues
30: Including chain 2 in system: 66 atoms 4 residues
30: Including chain 3 in system: 61 atoms 3 residues
30: Including chain 4 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (245 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 25 donors and 23 acceptors were found.
30: There are 41 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 256, now 256
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 652 pairs
30: Before cleaning: 662 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 12 cmap torsion pairs
30: There are 662 dihedrals, 47 impropers, 460 angles
30: 649 pairs, 256 bonds and 0 virtual sites
30: Total mass 1864.131 a.m.u.
30: Total charge 0.000 e
30: Writing topology
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records and chain id changing.
30:
30: Merged chains into joint molecule definitions at 1 places.
30:
30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 16 127
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (127 atoms, 16 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus MET-12: COO-
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 16 residues with 255 atoms
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (1681 ms)
30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
30: All occupancies are one
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
30:
Atomtype 1
Atomtype 2
Atomtype 3
Atomtype 4
Atomtype 5
Atomtype 6
Atomtype 7
Atomtype 8
Atomtype 9
Atomtype 10
Atomtype 11
Atomtype 12
Atomtype 13
Atomtype 14
Atomtype 15
Atomtype 16
Atomtype 17
Atomtype 18
Atomtype 19
Atomtype 20
Atomtype 21
Atomtype 22
Atomtype 23
Atomtype 24
Atomtype 25
Atomtype 26
Atomtype 27
Atomtype 28
Atomtype 29
Atomtype 30
Atomtype 31
Atomtype 32
Atomtype 33
Atomtype 34
Atomtype 35
Atomtype 36
Atomtype 37
Atomtype 38
Atomtype 39
Atomtype 40
Atomtype 41
Atomtype 42
Atomtype 43
Atomtype 44
Atomtype 45
Atomtype 46
Atomtype 47
Atomtype 48
Atomtype 49
Atomtype 50
Atomtype 51
Atomtype 52
Atomtype 53
Atomtype 54
Atomtype 55
Atomtype 56
Atomtype 57
Atomtype 58
Atomtype 59
Atomtype 60
Atomtype 61
Atomtype 62
Atomtype 63
Atomtype 64
Atomtype 65
Atomtype 66
Atomtype 67
Atomtype 68
Atomtype 69
Atomtype 70
Atomtype 71
Atomtype 72
Atomtype 73
Atomtype 74
Atomtype 75
Atomtype 76
Atomtype 77
Atomtype 78
Atomtype 79
Atomtype 80
Atomtype 81
Atomtype 82
Atomtype 83
Atomtype 84
Atomtype 85
Atomtype 86
Atomtype 87
Atomtype 88
Atomtype 89
Atomtype 90
Atomtype 91
Atomtype 92
Atomtype 93
Atomtype 94
Atomtype 95
Atomtype 96
Atomtype 97
Atomtype 98
Atomtype 99
Atomtype 100
Atomtype 101
Atomtype 102
Atomtype 103
Atomtype 104
Atomtype 105
Atomtype 106
Atomtype 107
Atomtype 108
Atomtype 109
Atomtype 110
Atomtype 111
Atomtype 112
Atomtype 113
Atomtype 114
Atomtype 115
Atomtype 116
Atomtype 117
Atomtype 118
Atomtype 119
Atomtype 120
Atomtype 121
Atomtype 122
Atomtype 123
Atomtype 124
Atomtype 125
Atomtype 126
Atomtype 127
Atomtype 128
Atomtype 129
Atomtype 130
Atomtype 131
Atomtype 132
Atomtype 133
Atomtype 134
Atomtype 135
Atomtype 136
Atomtype 137
Atomtype 138
Atomtype 139
Atomtype 140
Atomtype 141
Atomtype 142
Atomtype 143
Atomtype 144
Atomtype 145
Atomtype 146
Atomtype 147
Atomtype 148
Atomtype 149
Atomtype 150
Atomtype 151
Atomtype 152
Atomtype 153
Atomtype 154
Atomtype 155
Atomtype 156
Atomtype 157
Atomtype 158
Atomtype 159
Atomtype 160
Atomtype 161
Atomtype 162
Atomtype 163
Atomtype 164
Atomtype 165
Atomtype 166
Atomtype 167
Atomtype 168
Atomtype 169
Atomtype 170
Atomtype 171
Atomtype 172
Atomtype 173
Atomtype 174
Atomtype 175
Atomtype 176
Atomtype 177
Atomtype 178
Atomtype 179
Atomtype 180
Atomtype 181
Atomtype 182
Atomtype 183
Atomtype 184
Atomtype 185
Atomtype 186
Atomtype 187
Atomtype 188
Atomtype 189
Atomtype 190
Atomtype 191
Atomtype 192
Atomtype 193
Atomtype 194
Atomtype 195
Atomtype 196
Atomtype 197
Atomtype 198
Atomtype 199
Atomtype 200
Atomtype 201
Atomtype 202
Atomtype 203
Atomtype 204
Atomtype 205
Atomtype 206
Atomtype 207
Atomtype 208
Atomtype 209
Atomtype 210
Atomtype 211
Atomtype 212
Atomtype 213
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
30:
Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
30:
Residue 45
Residue 46
Residue 47
Residue 48
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
30:
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
30:
Residue 61
Residue 62
Residue 63
Residue 64
30: Sorting it all out...
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
30: Analysing hydrogen-bonding network for automated assignment of histidine
30: protonation. 14 donors and 15 acceptors were found.
30: There are 20 hydrogen bonds
30: Will use HISE for residue 8
30: 8 out of 8 lines of specbond.dat converted successfully
30: Special Atom Distance matrix:
30: CYS3 HIS8
30: SG9 NE251
30: HIS8 NE251 1.055
30: MET12 SD83 0.763 0.990
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 173, now 173
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 441 pairs
30: Before cleaning: 446 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 9 cmap torsion pairs
30: There are 446 dihedrals, 29 impropers, 312 angles
30: 438 pairs, 173 bonds and 0 virtual sites
30: Total mass 1262.488 a.m.u.
30: Total charge -1.000 e
30: Writing topology
30: 8 out of 8 lines of specbond.dat converted successfully
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
30: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
30: Making bonds...
30: Number of bonds was 83, now 83
30: Generating angles, dihedrals and pairs...
30: Before cleaning: 211 pairs
30: Before cleaning: 216 dihedrals
30: Keeping all generated dihedrals
30: Making cmap torsions...
30: There are 3 cmap torsion pairs
30: There are 216 dihedrals, 18 impropers, 148 angles
30: 211 pairs, 83 bonds and 0 virtual sites
30: Total mass 601.643 a.m.u.
30: Total charge 1.000 e
30: Writing topology
30: Now there are 255 atoms and 16 residues
30: Total mass in system 1864.131 a.m.u.
30: Total charge in system 0.000 e
30:
30: Writing coordinate file...
30:
30: Using the Charmm27 force field in directory charmm27.ff
30:
30: going to rename charmm27.ff/aminoacids.r2b
30: going to rename charmm27.ff/rna.r2b
30: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
30: Analyzing pdb file
30: Splitting chemical chains based on TER records and chain id changing.
30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
30:
30: chain #res #atoms
30: 1 'A' 11 86
30: 2 'C' 5 41
30:
30: Reading residue database... (Charmm27)
30: Processing chain 1 'A' (86 atoms, 11 residues)
30: Identified residue ALA2 as a starting terminus.
30: Identified residue MET12 as a ending terminus.
30: Start terminus ALA-2: NH3+
30: End terminus MET-12: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 11 residues with 172 atoms
30: Chain time...
30: Processing chain 2 'C' (41 atoms, 5 residues)
30: Identified residue ASN13 as a starting terminus.
30: Identified residue SER17 as a ending terminus.
30: Start terminus ASN-13: NH3+
30: End terminus SER-17: COO-
30: Checking for duplicate atoms....
30: Generating any missing hydrogen atoms and/or adding termini.
30: Now there are 5 residues with 83 atoms
30: Chain time...
30: Including chain 1 in system: 172 atoms 11 residues
30: Including chain 2 in system: 83 atoms 5 residues
30: --------- PLEASE NOTE ------------
30: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
30: The Charmm27 force field and the tip3p water model are used.
30: --------- ETON ESAELP ------------
30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (215 ms)
30: [----------] 8 tests from ChainSep/Pdb2gmxTest (7387 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 80 tests from 6 test cases ran. (110981 ms total)
30: [ PASSED ] 80 tests.
30/40 Test #30: Pdb2gmxTest ...................... Passed 111.05 sec
test 31
Start 31: CorrelationsTest
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
31: Test timeout computed to be: 30
31: [==========] Running 11 tests from 2 test cases.
31: [----------] Global test environment set-up.
31: [----------] 10 tests from AutocorrTest
31: [ RUN ] AutocorrTest.EacNormal
31: [ OK ] AutocorrTest.EacNormal (11 ms)
31: [ RUN ] AutocorrTest.EacNoNormalize
31: [ OK ] AutocorrTest.EacNoNormalize (6 ms)
31: [ RUN ] AutocorrTest.EacCos
31: [ OK ] AutocorrTest.EacCos (10 ms)
31: [ RUN ] AutocorrTest.EacVector
31: [ OK ] AutocorrTest.EacVector (21 ms)
31: [ RUN ] AutocorrTest.EacRcross
31: [ OK ] AutocorrTest.EacRcross (7 ms)
31: [ RUN ] AutocorrTest.EacP0
31: [ OK ] AutocorrTest.EacP0 (21 ms)
31: [ RUN ] AutocorrTest.EacP1
31: [ OK ] AutocorrTest.EacP1 (21 ms)
31: [ RUN ] AutocorrTest.EacP2
31: [ OK ] AutocorrTest.EacP2 (40 ms)
31: [ RUN ] AutocorrTest.EacP3
31: [ OK ] AutocorrTest.EacP3 (18 ms)
31: [ RUN ] AutocorrTest.EacP4
31: [ OK ] AutocorrTest.EacP4 (24 ms)
31: [----------] 10 tests from AutocorrTest (185 ms total)
31:
31: [----------] 1 test from ManyAutocorrelationTest
31: [ RUN ] ManyAutocorrelationTest.Empty
31: [ OK ] ManyAutocorrelationTest.Empty (1 ms)
31: [----------] 1 test from ManyAutocorrelationTest (1 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 11 tests from 2 test cases ran. (193 ms total)
31: [ PASSED ] 11 tests.
31/40 Test #31: CorrelationsTest ................. Passed 0.23 sec
test 32
Start 32: AnalysisDataUnitTests
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
32: Test timeout computed to be: 30
32: [==========] Running 69 tests from 14 test cases.
32: [----------] Global test environment set-up.
32: [----------] 3 tests from AnalysisDataInitializationTest
32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms)
32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
32: [----------] 3 tests from AnalysisDataInitializationTest (1 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms)
32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms)
32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/0 (14 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (3 ms)
32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms)
32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (1 ms)
32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/1 (16 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms)
32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (1 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/2 (18 ms total)
32:
32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (3 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (2 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms)
32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms)
32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms)
32: [----------] 8 tests from AnalysisDataCommonTest/3 (18 ms total)
32:
32: [----------] 4 tests from AnalysisArrayDataTest
32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
32: [ RUN ] AnalysisArrayDataTest.StorageWorks
32: [ OK ] AnalysisArrayDataTest.StorageWorks (1 ms)
32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
32: [----------] 4 tests from AnalysisArrayDataTest (4 ms total)
32:
32: [----------] 6 tests from AverageModuleTest
32: [ RUN ] AverageModuleTest.BasicTest
32: [ OK ] AverageModuleTest.BasicTest (3 ms)
32: [ RUN ] AverageModuleTest.HandlesMultipointData
32: [ OK ] AverageModuleTest.HandlesMultipointData (4 ms)
32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (3 ms)
32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (3 ms)
32: [ RUN ] AverageModuleTest.CanCustomizeXAxis
32: [ OK ] AverageModuleTest.CanCustomizeXAxis (3 ms)
32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (3 ms)
32: [----------] 6 tests from AverageModuleTest (20 ms total)
32:
32: [----------] 2 tests from FrameAverageModuleTest
32: [ RUN ] FrameAverageModuleTest.BasicTest
32: [ OK ] FrameAverageModuleTest.BasicTest (3 ms)
32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (4 ms)
32: [----------] 2 tests from FrameAverageModuleTest (7 ms total)
32:
32: [----------] 7 tests from AnalysisHistogramSettingsTest
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
32: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
32:
32: [----------] 2 tests from SimpleHistogramModuleTest
32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (5 ms)
32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (5 ms)
32: [----------] 2 tests from SimpleHistogramModuleTest (10 ms total)
32:
32: [----------] 3 tests from WeightedHistogramModuleTest
32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (4 ms)
32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (4 ms)
32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (5 ms)
32: [----------] 3 tests from WeightedHistogramModuleTest (15 ms total)
32:
32: [----------] 3 tests from BinAverageModuleTest
32: [ RUN ] BinAverageModuleTest.ComputesCorrectly
32: [ OK ] BinAverageModuleTest.ComputesCorrectly (4 ms)
32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (4 ms)
32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (4 ms)
32: [----------] 3 tests from BinAverageModuleTest (12 ms total)
32:
32: [----------] 4 tests from AbstractAverageHistogramTest
32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (5 ms)
32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (5 ms)
32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (4 ms)
32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (4 ms)
32: [----------] 4 tests from AbstractAverageHistogramTest (18 ms total)
32:
32: [----------] 3 tests from LifetimeModuleTest
32: [ RUN ] LifetimeModuleTest.BasicTest
32: [ OK ] LifetimeModuleTest.BasicTest (3 ms)
32: [ RUN ] LifetimeModuleTest.CumulativeTest
32: [ OK ] LifetimeModuleTest.CumulativeTest (3 ms)
32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (3 ms)
32: [----------] 3 tests from LifetimeModuleTest (9 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 69 tests from 14 test cases ran. (163 ms total)
32: [ PASSED ] 69 tests.
32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.22 sec
test 33
Start 33: SelectionUnitTests
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
33: Test timeout computed to be: 30
33: [==========] Running 190 tests from 10 test cases.
33: [----------] Global test environment set-up.
33: [----------] 1 test from IndexGroupTest
33: [ RUN ] IndexGroupTest.RemovesDuplicates
33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
33: [----------] 1 test from IndexGroupTest (0 ms total)
33:
33: [----------] 15 tests from IndexBlockTest
33: [ RUN ] IndexBlockTest.CreatesUnknownBlock
33: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms)
33: [ RUN ] IndexBlockTest.CreatesAtomBlock
33: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesResidueBlock
33: [ OK ] IndexBlockTest.CreatesResidueBlock (1 ms)
33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock
33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (0 ms)
33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion
33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (1 ms)
33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion
33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (0 ms)
33: [ RUN ] IndexBlockTest.CreatesSingleBlock
33: [ OK ] IndexBlockTest.CreatesSingleBlock (1 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (1 ms)
33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
33: [----------] 15 tests from IndexBlockTest (5 ms total)
33:
33: [----------] 11 tests from IndexMapTest
33: [ RUN ] IndexMapTest.InitializesAtomBlock
33: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms)
33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
33: [ RUN ] IndexMapTest.InitializesMoleculeBlock
33: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
33: [ RUN ] IndexMapTest.MapsSingleBlock
33: [ OK ] IndexMapTest.MapsSingleBlock (0 ms)
33: [ RUN ] IndexMapTest.MapsResidueBlocks
33: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (1 ms)
33: [ RUN ] IndexMapTest.HandlesMultipleRequests
33: [ OK ] IndexMapTest.HandlesMultipleRequests (2 ms)
33: [----------] 11 tests from IndexMapTest (9 ms total)
33:
33: [----------] 15 tests from NeighborhoodSearchTest
33: [ RUN ] NeighborhoodSearchTest.SimpleSearch
33: [ OK ] NeighborhoodSearchTest.SimpleSearch (67 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (75 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchBox
33: [ OK ] NeighborhoodSearchTest.GridSearchBox (11 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (53 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (32 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (18 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (15 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (210 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (18 ms)
33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
33: [----------] 15 tests from NeighborhoodSearchTest (505 ms total)
33:
33: [----------] 12 tests from PositionCalculationTest
33: [ RUN ] PositionCalculationTest.ComputesAtomPositions
33: [ OK ] PositionCalculationTest.ComputesAtomPositions (2 ms)
33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms)
33: [ RUN ] PositionCalculationTest.ComputesPositionMask
33: [ OK ] PositionCalculationTest.ComputesPositionMask (1 ms)
33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (2 ms)
33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (1 ms)
33: [----------] 12 tests from PositionCalculationTest (15 ms total)
33:
33: [----------] 30 tests from SelectionCollectionTest
33: [ RUN ] SelectionCollectionTest.HandlesNoSelections
33: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions
33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms)
33: [----------] 30 tests from SelectionCollectionTest (45 ms total)
33:
33: [----------] 14 tests from SelectionCollectionInteractiveTest
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (2 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms)
33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
33: [----------] 14 tests from SelectionCollectionInteractiveTest (20 ms total)
33:
33: [----------] 66 tests from SelectionCollectionDataTest
33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResnr
33: [ OK ] SelectionCollectionDataTest.HandlesResnr (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesChain
33: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMass
33: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesCharge
33: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBeta
33: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesResname
33: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (15 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (6 ms)
33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (7 ms)
33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (7 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (5 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (6 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (2 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (3 ms)
33: [----------] 66 tests from SelectionCollectionDataTest (229 ms total)
33:
33: [----------] 17 tests from SelectionOptionTest
33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (2 ms)
33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
33: [ RUN ] SelectionOptionTest.ChecksEmptySelections
33: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooManySelections
33: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesAdjuster
33: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms)
33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
33: [----------] 17 tests from SelectionOptionTest (20 ms total)
33:
33: [----------] 9 tests from SelectionFileOptionTest
33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (2 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
33: [----------] 9 tests from SelectionFileOptionTest (11 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 190 tests from 10 test cases ran. (859 ms total)
33: [ PASSED ] 190 tests.
33/40 Test #33: SelectionUnitTests ............... Passed 0.92 sec
test 34
Start 34: TrajectoryAnalysisUnitTests
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
34: Test timeout computed to be: 30
34: [==========] Running 74 tests from 14 test cases.
34: [----------] Global test environment set-up.
34: [----------] 5 tests from ClustsizeTest
34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
34: There is one group in the index
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 24
34: cmid: 2, cmax: 4, max_size: 6
34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (12 ms)
34: [ RUN ] ClustsizeTest.NoMolShortCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
34: There is one group in the index
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 24
34: cmid: 1, cmax: 6, max_size: 6
34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (10 ms)
34: [ RUN ] ClustsizeTest.MolDefaultCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 2, cmax: 4, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (12 ms)
34: [ RUN ] ClustsizeTest.MolShortCutoff
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 1, cmax: 6, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (11 ms)
34: [ RUN ] ClustsizeTest.MolCSize
34: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
34: '', 24 atoms
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Total number of atoms in clusters = 8
34: cmid: 2, cmax: 4, max_size: 2
34: 50%100%cmid: 2, cmax: 6, max_size: 2
34: 50%100%[ OK ] ClustsizeTest.MolCSize (27 ms)
34: [----------] 5 tests from ClustsizeTest (73 ms total)
34:
34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (4 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
34: Reading frames from gro file 'Test system', 8 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (15 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
34: Reading frames from gro file 'Test system', 8 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (15 ms)
34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms)
34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (36 ms total)
34:
34: [----------] 11 tests from AngleModuleTest
34: [ RUN ] AngleModuleTest.ComputesSimpleAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesSimpleAngles (16 ms)
34: [ RUN ] AngleModuleTest.ComputesDihedrals
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesDihedrals (16 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (16 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (13 ms)
34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (13 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (15 ms)
34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
34: Reading frames from gro file 'Test system for different angles', 33 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (15 ms)
34: [ RUN ] AngleModuleTest.ComputesMultipleAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.ComputesMultipleAngles (15 ms)
34: [ RUN ] AngleModuleTest.HandlesDynamicSelections
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesDynamicSelections (14 ms)
34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (16 ms)
34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (20 ms)
34: [----------] 11 tests from AngleModuleTest (171 ms total)
34:
34: [----------] 3 tests from DistanceModuleTest
34: [ RUN ] DistanceModuleTest.ComputesDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2:
34: Number of samples: 5
34: Average distance: 1.43246 nm
34: Standard deviation: 0.96700 nm
34: [ OK ] DistanceModuleTest.ComputesDistances (23 ms)
34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2:
34: Number of samples: 5
34: Average distance: 1.43246 nm
34: Standard deviation: 0.96700 nm
34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
34: Number of samples: 4
34: Average distance: 1.81066 nm
34: Standard deviation: 0.79289 nm
34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (25 ms)
34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: atomname S1 S2 and res_cog x < 2.8:
34: Number of samples: 3
34: Average distance: 1.72076 nm
34: Standard deviation: 1.24839 nm
34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (24 ms)
34: [----------] 3 tests from DistanceModuleTest (73 ms total)
34:
34: [----------] 2 tests from FreeVolumeModuleTest
34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for CO2-RM. Set to zero.
34: Could not determine VDW radius for 40 particles. These were set to zero.
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: cutoff = 0.18 nm
34: probe_radius = 0 nm
34: seed = 13
34: ninsert = 1000 probes per nm^3
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
34: van der Spoel and Luciano T. Costa
34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
34: -------- -------- --- Thank You --- -------- --------
34:
34: Free volume 38.02 +/- 0.00 %
34: Total volume 68.92 +/- 0.00 nm^3
34: Number of molecules 340 total mass 63491.38 Dalton
34: Average molar mass: 186.74 Dalton
34: Density rho: 1529.71 +/- 0.00 nm^3
34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
34: Fractional free volume 0.194 +/- 0.000
34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (563 ms)
34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: cutoff = 0.18 nm
34: probe_radius = 0 nm
34: seed = 17
34: ninsert = 1000 probes per nm^3
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
34: van der Spoel and Luciano T. Costa
34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
34: -------- -------- --- Thank You --- -------- --------
34:
34: Free volume 38.48 +/- 0.00 %
34: Total volume 68.92 +/- 0.00 nm^3
34: Number of molecules 340 total mass 63491.38 Dalton
34: Average molar mass: 186.74 Dalton
34: Density rho: 1529.71 +/- 0.00 nm^3
34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
34: Fractional free volume 0.200 +/- 0.000
34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (486 ms)
34: [----------] 2 tests from FreeVolumeModuleTest (1049 ms total)
34:
34: [----------] 7 tests from PairDistanceModuleTest
34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (17 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (16 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (16 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (15 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (14 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (14 ms)
34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (14 ms)
34: [----------] 7 tests from PairDistanceModuleTest (107 ms total)
34:
34: [----------] 5 tests from RdfModuleTest
34: [ RUN ] RdfModuleTest.BasicTest
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.BasicTest (107 ms)
34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
34:
Reading frame 0 time 0.000
Last frame 0 time 0.000
34: Analyzed 1 frames, last time 0.000
34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (86 ms)
34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (135 ms)
34: [ RUN ] RdfModuleTest.CalculatesSurf
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.CalculatesSurf (76 ms)
34: [ RUN ] RdfModuleTest.CalculatesXY
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] RdfModuleTest.CalculatesXY (156 ms)
34: [----------] 5 tests from RdfModuleTest (563 ms total)
34:
34: [----------] 5 tests from SasaModuleTest
34: [ RUN ] SasaModuleTest.BasicTest
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.BasicTest (53 ms)
34: [ RUN ] SasaModuleTest.HandlesSelectedResidues
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesSelectedResidues (33 ms)
34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (32 ms)
34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (38 ms)
34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
34: Michael Scharf
34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
34: of Surface Area and Volume and to Dot Surface Contouring of Molecular
34: Assemblies
34: J. Comp. Chem. 16 (1995) pp. 273-284
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
34: from the source below. This means the results may be different
34: compared to previous GROMACS versions.
34:
34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
34: A. Bondi
34: van der Waals Volumes and Radii
34: J. Phys. Chem. 68 (1964) pp. 441-451
34: -------- -------- --- Thank You --- -------- --------
34:
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (39 ms)
34: [----------] 5 tests from SasaModuleTest (201 ms total)
34:
34: [----------] 8 tests from SelectModuleTest
34: [ RUN ] SelectModuleTest.BasicTest
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.BasicTest (32 ms)
34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (28 ms)
34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (27 ms)
34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (27 ms)
34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (27 ms)
34: [ RUN ] SelectModuleTest.NormalizesSizes
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.NormalizesSizes (18 ms)
34: [ RUN ] SelectModuleTest.WritesResidueNumbers
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.WritesResidueNumbers (17 ms)
34: [ RUN ] SelectModuleTest.WritesResidueIndices
34:
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34: Analyzed topology coordinates
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] SelectModuleTest.WritesResidueIndices (18 ms)
34: [----------] 8 tests from SelectModuleTest (198 ms total)
34:
34: [----------] 10 tests from SurfaceAreaTest
34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (6 ms)
34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (5 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints12
34: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints32
34: [ OK ] SurfaceAreaTest.SurfacePoints32 (2 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints42
34: [ OK ] SurfaceAreaTest.SurfacePoints42 (3 ms)
34: [ RUN ] SurfaceAreaTest.SurfacePoints122
34: [ OK ] SurfaceAreaTest.SurfacePoints122 (5 ms)
34: [ RUN ] SurfaceAreaTest.Computes100Points
34: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (13 ms)
34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (16 ms)
34: [----------] 10 tests from SurfaceAreaTest (57 ms total)
34:
34: [----------] 4 tests from TopologyInformation
34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
34: [ RUN ] TopologyInformation.WorksWithGroFile
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TopologyInformation.WorksWithGroFile (21 ms)
34: [ RUN ] TopologyInformation.WorksWithPdbFile
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TopologyInformation.WorksWithPdbFile (20 ms)
34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
34:
34: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]:
34: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
34: scheme was introduced, but the group scheme was still the default. The
34: default is now the Verlet scheme, so you will observe different behaviour.
34:
34:
34: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: For a correct single-point energy evaluation with nsteps = 0, use
34: continuation = yes to avoid constraining the input coordinates.
34:
34: Setting the LD random seed to -215529876
34: Generated 330891 of the 330891 non-bonded parameter combinations
34: Generating 1-4 interactions: fudge = 0.5
34: Generated 330891 of the 330891 1-4 parameter combinations
34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
34:
34: NOTE 3 [file lysozyme.top, line 1465]:
34: System has non-zero total charge: 2.000000
34: Total charge should normally be an integer. See
34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
34: for discussion on how close it should be to an integer.
34:
34:
34:
34: Removing all charge groups because cutoff-scheme=Verlet
34: Number of degrees of freedom in T-Coupling group rest is 465.00
34:
34: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: NVE simulation with an initial temperature of zero: will use a Verlet
34: buffer of 10%. Check your energy drift!
34:
34:
34: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
34: You are using a plain Coulomb cut-off, which might produce artifacts.
34: You might want to consider using PME electrostatics.
34:
34:
34:
34: There were 5 notes
34: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.3 (double precision)
34: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.3 (double precision)
34: Analysing residue names:
34: There are: 10 Protein residues
34: Analysing Protein...
34: This run will generate roughly 0 Mb of data
34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (1648 ms)
34: [----------] 4 tests from TopologyInformation (1690 ms total)
34:
34: [----------] 4 tests from TrajectoryModuleTest
34: [ RUN ] TrajectoryModuleTest.BasicTest
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.BasicTest (20 ms)
34: [ RUN ] TrajectoryModuleTest.PlotsXOnly
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.PlotsXOnly (18 ms)
34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (16 ms)
34: [ RUN ] TrajectoryModuleTest.HandlesNoForces
34: Reading frames from gro file 'Test system', 15 atoms.
34:
Reading frame 0 time 0.000
34: WARNING: If there are molecules in the input trajectory file
34: that are broken across periodic boundaries, they
34: cannot be made whole (or treated as whole) without
34: you providing a run input file.
34:
34:
Reading frame 1 time 0.000
Last frame 1 time 0.000
34: Analyzed 2 frames, last time 0.000
34:
34: WARNING: Masses and atomic (Van der Waals) radii will be guessed
34: based on residue and atom names, since they could not be
34: definitively assigned from the information in your input
34: files. These guessed numbers might deviate from the mass
34: and radius of the atom type. Please check the output
34: files if necessary.
34:
34: [ OK ] TrajectoryModuleTest.HandlesNoForces (17 ms)
34: [----------] 4 tests from TrajectoryModuleTest (72 ms total)
34:
34: [----------] 5 tests from UnionFinderTest
34: [ RUN ] UnionFinderTest.WorksEmpty
34: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
34: [ RUN ] UnionFinderTest.BasicMerges
34: [ OK ] UnionFinderTest.BasicMerges (0 ms)
34: [ RUN ] UnionFinderTest.LargerMerges
34: [ OK ] UnionFinderTest.LargerMerges (0 ms)
34: [ RUN ] UnionFinderTest.LongRightMerge
34: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
34: [ RUN ] UnionFinderTest.LongLeftMerge
34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
34: [----------] 5 tests from UnionFinderTest (0 ms total)
34:
34: [----------] 1 test from MappedUnionFinderTest
34: [ RUN ] MappedUnionFinderTest.BasicMerges
34: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
34: [----------] 1 test from MappedUnionFinderTest (1 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 74 tests from 14 test cases ran. (4292 ms total)
34: [ PASSED ] 74 tests.
34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 4.35 sec
test 35
Start 35: EnergyAnalysisUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 7 tests from 4 test cases.
35: [----------] Global test environment set-up.
35: [----------] 1 test from DhdlTest
35: [ RUN ] DhdlTest.ExtractDhdl
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
35: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
35: Note: file tpx version 110, software tpx version 116
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
35:
35:
35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
35: [ OK ] DhdlTest.ExtractDhdl (36 ms)
35: [----------] 1 test from DhdlTest (38 ms total)
35:
35: [----------] 1 test from OriresTest
35: [ RUN ] OriresTest.ExtractOrires
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
35: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
35: Note: file tpx version 111, software tpx version 116
35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
35: End your selection with 0
35: Selecting all 7 orientation restraints
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
35: [ OK ] OriresTest.ExtractOrires (42 ms)
35: [----------] 1 test from OriresTest (42 ms total)
35:
35: [----------] 3 tests from EnergyTest
35: [ RUN ] EnergyTest.ExtractEnergy
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
35: [ OK ] EnergyTest.ExtractEnergy (12 ms)
35: [ RUN ] EnergyTest.ExtractEnergyByNumber
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
35: Pres. DC -268.49 3 8.52175 13.2804 (bar)
35: [ OK ] EnergyTest.ExtractEnergyByNumber (11 ms)
35: [ RUN ] EnergyTest.ExtractEnergyMixed
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
35: Select the terms you want from the following list by
35: selecting either (part of) the name or the number or a combination.
35: End your selection with an empty line or a zero.
35: -------------------------------------------------------------------
35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
35: 13 Box-Z 14 Volume 15 Density 16 pV
35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
35:
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: [ OK ] EnergyTest.ExtractEnergyMixed (13 ms)
35: [----------] 3 tests from EnergyTest (38 ms total)
35:
35: [----------] 2 tests from ViscosityTest
35: [ RUN ] ViscosityTest.EinsteinViscosity
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Pres-XX 20.2092 65 717.193 185.978 (bar)
35: Pres-XY -47.7351 39 372.522 207.456 (bar)
35: Pres-XZ 11.477 31 379.79 6.80818 (bar)
35: Pres-YX -47.7106 39 372.525 207.5 (bar)
35: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
35: Pres-YZ -41.3534 45 401.216 114.663 (bar)
35: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
35: Pres-ZY -41.3119 45 401.196 114.743 (bar)
35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
35: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: [ OK ] ViscosityTest.EinsteinViscosity (30 ms)
35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
35: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
35:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
35:
35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
35: All statistics are over 5001 points
35:
35: Energy Average Err.Est. RMSD Tot-Drift
35: -------------------------------------------------------------------------------
35: Pres-XX 20.2092 65 717.193 185.978 (bar)
35: Pres-XY -47.7351 39 372.522 207.456 (bar)
35: Pres-XZ 11.477 31 379.79 6.80818 (bar)
35: Pres-YX -47.7106 39 372.525 207.5 (bar)
35: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
35: Pres-YZ -41.3534 45 401.216 114.663 (bar)
35: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
35: Pres-ZY -41.3119 45 401.196 114.743 (bar)
35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
35: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
35: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (24 ms)
35: [----------] 2 tests from ViscosityTest (55 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 7 tests from 4 test cases ran. (174 ms total)
35: [ PASSED ] 7 tests.
35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.22 sec
test 36
Start 36: ToolUnitTests
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 4 tests from 1 test case.
36: [----------] Global test environment set-up.
36: [----------] 4 tests from ReportMethodsTest
36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (1 ms)
36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
36: [ RUN ] ReportMethodsTest.WritesCorrectInformation
36:
36: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]:
36: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
36: scheme was introduced, but the group scheme was still the default. The
36: default is now the Verlet scheme, so you will observe different behaviour.
36:
36:
36: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: For a correct single-point energy evaluation with nsteps = 0, use
36: continuation = yes to avoid constraining the input coordinates.
36:
36: Setting the LD random seed to -718994430
36: Generated 330891 of the 330891 non-bonded parameter combinations
36: Generating 1-4 interactions: fudge = 0.5
36: Generated 330891 of the 330891 1-4 parameter combinations
36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
36:
36: NOTE 3 [file lysozyme.top, line 1465]:
36: System has non-zero total charge: 2.000000
36: Total charge should normally be an integer. See
36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
36: for discussion on how close it should be to an integer.
36:
36:
36:
36: Removing all charge groups because cutoff-scheme=Verlet
36: Number of degrees of freedom in T-Coupling group rest is 465.00
36:
36: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: NVE simulation with an initial temperature of zero: will use a Verlet
36: buffer of 10%. Check your energy drift!
36:
36:
36: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]:
36: You are using a plain Coulomb cut-off, which might produce artifacts.
36: You might want to consider using PME electrostatics.
36:
36:
36:
36: There were 5 notes
36: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.3 (double precision)
36: Analysing residue names:
36: There are: 10 Protein residues
36: Analysing Protein...
36: This run will generate roughly 0 Mb of data
36: [ OK ] ReportMethodsTest.WritesCorrectInformation (1669 ms)
36: [ RUN ] ReportMethodsTest.ToolEndToEndTest
36:
36: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]:
36: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
36: scheme was introduced, but the group scheme was still the default. The
36: default is now the Verlet scheme, so you will observe different behaviour.
36:
36:
36: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: For a correct single-point energy evaluation with nsteps = 0, use
36: continuation = yes to avoid constraining the input coordinates.
36:
36: Setting the LD random seed to 1132498207
36: Generated 330891 of the 330891 non-bonded parameter combinations
36: Generating 1-4 interactions: fudge = 0.5
36: Generated 330891 of the 330891 1-4 parameter combinations
36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
36:
36: NOTE 3 [file lysozyme.top, line 1465]:
36: System has non-zero total charge: 2.000000
36: Total charge should normally be an integer. See
36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
36: for discussion on how close it should be to an integer.
36:
36:
36:
36: Removing all charge groups because cutoff-scheme=Verlet
36: Number of degrees of freedom in T-Coupling group rest is 465.00
36:
36: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: NVE simulation with an initial temperature of zero: will use a Verlet
36: buffer of 10%. Check your energy drift!
36:
36:
36: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]:
36: You are using a plain Coulomb cut-off, which might produce artifacts.
36: You might want to consider using PME electrostatics.
36:
36:
36:
36: There were 5 notes
36: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.3 (double precision)
36: Analysing residue names:
36: There are: 10 Protein residues
36: Analysing Protein...
36: This run will generate roughly 0 Mb of data
36: section: Methods
36: subsection: Simulation system
36: A system of 1 molecules (156 atoms) was simulated.
36:
36: subsection: Simulation settings
36: A total of 0 ns were simulated with a time step of 1 fs.
36: Neighbor searching was performed every 10 steps.
36: The Cut-off algorithm was used for electrostatic interactions.
36: with a cut-off of 1 nm.
36: A single cut-off of 1.1 nm was used for Van der Waals interactions.
36: [ OK ] ReportMethodsTest.ToolEndToEndTest (1579 ms)
36: [----------] 4 tests from ReportMethodsTest (3249 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 4 tests from 1 test case ran. (3249 ms total)
36: [ PASSED ] 4 tests.
36/40 Test #36: ToolUnitTests .................... Passed 3.29 sec
test 37
Start 37: MdrunTests
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
37: Test timeout computed to be: 600
37: [==========] Running 29 tests from 11 test cases.
37: [----------] Global test environment set-up.
37: [----------] 1 test from GromppTest
37: [ RUN ] GromppTest.EmptyMdpFileWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1049363072
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 12.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: NVE simulation: will use the initial temperature of 1046.791 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37: [ OK ] GromppTest.EmptyMdpFileWorks (119 ms)
37: [----------] 1 test from GromppTest (119 ms total)
37:
37: [----------] 1 test from ImdTest
37: [ RUN ] ImdTest.ImdCanRun
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]:
37: The Berendsen thermostat does not generate the correct kinetic energy
37: distribution. You might want to consider using the V-rescale thermostat.
37:
37: Setting the LD random seed to 2091819181
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD).
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 50, rlist from 1.121 to 1.344
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: IMD: Enabled. This simulation will accept incoming IMD connections.
37: IMD: You chose a port number < 1. Will automatically assign a free port.
37: IMD: Pulling from IMD remote is enabled (-imdpull).
37: IMD: Turning on IMD - port for incoming requests is 0.
37: IMD: Setting up incoming socket.
37: IMD: Listening for IMD connection on port 52933.
37: IMD: -imdwait not set, starting simulation.
37: starting mdrun 'spc2'
37: 2 steps, 0.0 ps.
37: turning all bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.338 0.169 199.6
37: (ns/day) (hour/ns)
37: Performance: 6.132 3.914
37: [ OK ] ImdTest.ImdCanRun (279 ms)
37: [----------] 1 test from ImdTest (280 ms total)
37:
37: [----------] 2 tests from PmeTest
37: [ RUN ] PmeTest.ReproducesEnergies
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -508666563
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
37: NVE simulation: will use the initial temperature of 1046.791 K for
37: determining the Verlet buffer size
37:
37: Estimate for the relative computational load of the PME mesh part: 1.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
37: The optimal PME mesh load for parallel simulations is below 0.5
37: and for highly parallel simulations between 0.25 and 0.33,
37: for higher performance, increase the cut-off and the PME grid spacing.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: Calculating fourier grid dimensions for X Y Z
37: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.554 0.277 199.8
37: (ns/day) (hour/ns)
37: Performance: 6.541 3.669
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.530 0.265 199.9
37: (ns/day) (hour/ns)
37: Performance: 6.838 3.510
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37:
37: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
37: starting mdrun 'spc-and-methanol'
37: 20 steps, 0.0 ps.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.610 0.305 199.9
37: (ns/day) (hour/ns)
37: Performance: 5.947 4.035
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1132 ms)
37: [ RUN ] PmeTest.ScalesTheBox
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 111824582
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Searching the wall atom type(s)
37: Number of degrees of freedom in T-Coupling group rest is 13.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: NVE simulation: will use the initial temperature of 966.269 K for
37: determining the Verlet buffer size
37:
37: Estimate for the relative computational load of the PME mesh part: 1.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
37: The optimal PME mesh load for parallel simulations is below 0.5
37: and for highly parallel simulations between 0.25 and 0.33,
37: for higher performance, increase the cut-off and the PME grid spacing.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 0 steps, 0.0 ps.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.053 0.027 197.6
37: (ns/day) (hour/ns)
37: Performance: 3.224 7.443
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.269 K
37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: Calculating fourier grid dimensions for X Y Z
37: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
37: This run will generate roughly 0 Mb of data
37: [ OK ] PmeTest.ScalesTheBox (293 ms)
37: [----------] 2 tests from PmeTest (1426 ms total)
37:
37: [----------] 1 test from CompelTest
37: [ RUN ] CompelTest.SwapCanRun
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
37: The Berendsen thermostat does not generate the correct kinetic energy
37: distribution. You might want to consider using the V-rescale thermostat.
37:
37: Setting the LD random seed to -747345784
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein'
37: Excluding 3 bonded neighbours molecule type 'OCT'
37: Excluding 1 bonded neighbours molecule type 'NA'
37: Excluding 1 bonded neighbours molecule type 'CL'
37: Excluding 3 bonded neighbours molecule type 'Protein'
37: Excluding 3 bonded neighbours molecule type 'OCT'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Split0 group 'Ch0' contains 83 atoms.
37: Split1 group 'Ch1' contains 83 atoms.
37: Solvent group 'SOL' contains 11931 atoms.
37: Swap group 'NA+' contains 19 atoms.
37: Swap group 'CL-' contains 19 atoms.
37: Number of degrees of freedom in T-Coupling group System is 27869.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.3 (double precision)
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: SWAP: Determining initial numbers of ions per compartment.
37: SWAP: Setting pointers for checkpoint writing
37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
37: starting mdrun 'Channel_coco in octane membrane'
37: 2 steps, 0.0 ps.
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: turning all bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 1 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 5.463 2.732 200.0
37: (ns/day) (hour/ns)
37: Performance: 0.474 50.586
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.3 (double precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: SWAP: Setting pointers for checkpoint writing
37: SWAP: Copying channel fluxes from checkpoint file data
37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
37: starting mdrun 'Channel_coco in octane membrane'
37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 4.969 2.485 200.0
37: (ns/day) (hour/ns)
37: Performance: 0.522 46.019
37: [ OK ] CompelTest.SwapCanRun (8126 ms)
37: [----------] 1 test from CompelTest (8126 ms total)
37:
37: [----------] 6 tests from BondedInteractionsTest
37: [ RUN ] BondedInteractionsTest.NormalBondWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1285807345
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 2 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.003 0.002 191.0
37: (ns/day) (hour/ns)
37: Performance: 47.998 0.500
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalBondWorks (40 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 1765413677
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 2 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.003 0.002 191.0
37: (ns/day) (hour/ns)
37: Performance: 56.988 0.421
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (40 ms)
37: [ RUN ] BondedInteractionsTest.NormalAngleWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -2076872933
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 1 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.003 0.002 191.6
37: (ns/day) (hour/ns)
37: Performance: 52.240 0.459
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalAngleWorks (33 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -788870708
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37:
37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
37: In moleculetype 'butane' 1 atoms are not bound by a potential or
37: constraint to any other atom in the same moleculetype. Although
37: technically this might not cause issues in a simulation, this often means
37: that the user forgot to add a bond/potential/constraint or put multiple
37: molecules in the same moleculetype definition by mistake. Run with -v to
37: get information for each atom.
37:
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.003 0.002 191.8
37: (ns/day) (hour/ns)
37: Performance: 51.055 0.470
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (35 ms)
37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1013361907
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 191.9
37: (ns/day) (hour/ns)
37: Performance: 38.307 0.627
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (40 ms)
37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 179720510
37: Generated 3 of the 3 non-bonded parameter combinations
37: Excluding 3 bonded neighbours molecule type 'butane'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/butane1.gro'
37:
37: Reading frames from gro file 'A single butane', 4 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 191.9
37: (ns/day) (hour/ns)
37: Performance: 37.686 0.637
37: This run will generate roughly 0 Mb of data
37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (52 ms)
37: [----------] 6 tests from BondedInteractionsTest (242 ms total)
37:
37: [----------] 2 tests from MdrunTerminationTest
37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1570508952
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 1, rlist from 1.024 to 1
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 100 steps, 0.1 ps.
37:
37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.253 0.126 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.367 17.559
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.3 (double precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps
37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
37:
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps).
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.242 0.121 199.8
37: (ns/day) (hour/ns)
37: Performance: 2.137 11.228
37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (303 ms)
37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 315301032
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 9.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 1, rlist from 1.024 to 1
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 100 steps, 0.1 ps.
37:
37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.282 0.141 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.225 19.598
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.3 (double precision)
37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps
37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
37:
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps).
37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'.
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.269 0.135 199.9
37: (ns/day) (hour/ns)
37: Performance: 1.923 12.478
37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (317 ms)
37: [----------] 2 tests from MdrunTerminationTest (620 ms total)
37:
37: [----------] 4 tests from MimicTest
37: [ RUN ] MimicTest.OneQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -336877904
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.006 0.003 194.5
37: (ns/day) (hour/ns)
37: Performance: 29.626 0.810
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.OneQuantumMol (34 ms)
37: [ RUN ] MimicTest.AllQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 744532312
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.005 0.002 193.0
37: (ns/day) (hour/ns)
37: Performance: 36.048 0.666
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.AllQuantumMol (33 ms)
37: [ RUN ] MimicTest.TwoQuantumMol
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -739768830
37: Generated 10 of the 10 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 10 of the 10 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 21.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
37:
37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.004 0.002 193.3
37: (ns/day) (hour/ns)
37: Performance: 41.321 0.581
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.TwoQuantumMol (31 ms)
37: [ RUN ] MimicTest.BondCuts
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to 2056186165
37: Generated 2211 of the 2211 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 2211 of the 2211 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 66.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: NVE simulation: will use the initial temperature of 300.368 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/ala.gro'
37:
37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.005 0.003 194.9
37: (ns/day) (hour/ns)
37: Performance: 31.192 0.769
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37: [ OK ] MimicTest.BondCuts (88 ms)
37: [----------] 4 tests from MimicTest (186 ms total)
37:
37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
37: Setting the LD random seed to 581231094
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.334 0.167 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.034 23.203
37:
Reading frame 0 time 0.000
37: # Atoms 6
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (203 ms)
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
37: Setting the LD random seed to -1986863975
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.376 0.188 199.8
37: (ns/day) (hour/ns)
37: Performance: 0.918 26.151
37:
Reading frame 0 time 0.000
37: # Atoms 6
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (228 ms)
37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
37: Setting the LD random seed to -1449757724
37: Generated 3 of the 3 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 3 of the 3 1-4 parameter combinations
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 9.00
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
37: NVE simulation: will use the initial temperature of 2573.591 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc2'
37: 1 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.370 0.185 199.8
37: (ns/day) (hour/ns)
37: Performance: 0.934 25.702
37:
Reading frame 0 time 0.000
37: # Atoms 3
37:
Reading frame 1 time 0.001
Last frame 1 time 0.001
37:
37:
37: Item #frames Timestep (ps)
37: Step 2 0.001
37: Time 2 0.001
37: Lambda 0
37: Coords 2 0.001
37: Velocities 0
37: Forces 0
37: Box 2 0.001
37: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (217 ms)
37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (648 ms total)
37:
37: [----------] 3 tests from Checking/InitialConstraintsTest
37: [ RUN ] Checking/InitialConstraintsTest.Works/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1277524199
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.282 0.141 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.224 19.602
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (272 ms)
37: [ RUN ] Checking/InitialConstraintsTest.Works/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -926234760
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 3 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.253 0.127 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.362 17.617
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (274 ms)
37: [ RUN ] Checking/InitialConstraintsTest.Works/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: Integrator method md-vv-avek is implemented primarily for validation
37: purposes; for molecular dynamics, you should probably be using md or md-vv
37:
37: Setting the LD random seed to -1844678709
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group rest is 11.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: NVE simulation: will use the initial temperature of 1141.954 K for
37: determining the Verlet buffer size
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.3 (double precision)
37: Can not increase nstlist because an NVE ensemble is used
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 1 steps, 0.0 ps.
37: turning H bonds into constraints...
37: turning H bonds into constraints...
37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.287 0.144 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.203 19.947
37: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
37:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (257 ms)
37: [----------] 3 tests from Checking/InitialConstraintsTest (803 ms total)
37:
37: [----------] 3 tests from MdrunCanWrite/Trajectories
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 743582093
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.331 0.166 199.7
37: (ns/day) (hour/ns)
37: Performance: 3.644 6.586
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (294 ms)
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 487883143
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.519 0.259 199.9
37: (ns/day) (hour/ns)
37: Performance: 2.331 10.296
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (420 ms)
37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 342425901
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 6 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.323 0.162 199.7
37: (ns/day) (hour/ns)
37: Performance: 3.738 6.421
37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (277 ms)
37: [----------] 3 tests from MdrunCanWrite/Trajectories (991 ms total)
37:
37: [----------] 3 tests from MdrunCanWrite/NptTrajectories
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to -1385261991
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.268 0.134 199.7
37: (ns/day) (hour/ns)
37: Performance: 1.928 12.447
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (271 ms)
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 617416348
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.249 0.125 199.7
37: (ns/day) (hour/ns)
37: Performance: 2.081 11.532
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (257 ms)
37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]:
37: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
37: scheme was introduced, but the group scheme was still the default. The
37: default is now the Verlet scheme, so you will observe different behaviour.
37:
37: Setting the LD random seed to 1138986980
37: Generated 279 of the 1225 non-bonded parameter combinations
37: Excluding 2 bonded neighbours molecule type 'Methanol'
37: Excluding 2 bonded neighbours molecule type 'SOL'
37: Removing all charge groups because cutoff-scheme=Verlet
37: Number of degrees of freedom in T-Coupling group System is 12.00
37:
37: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 2 notes
37: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.3 (double precision)
37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
37:
37: Using 1 MPI thread
37: Using 2 OpenMP threads
37:
37:
37: NOTE: The number of threads is not equal to the number of (logical) cores
37: and the -pin option is set to auto: will not pin threads to cores.
37: This can lead to significant performance degradation.
37: Consider using -pin on (and -pinoffset in case you run multiple jobs).
37:
37: WARNING: Using the slow plain C kernels. This should
37: not happen during routine usage on supported platforms.
37: starting mdrun 'spc-and-methanol'
37: 2 steps, 0.0 ps.
37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
37: Note that mdrun will redetermine rlist based on the actual pair-list setup
37: This run will generate roughly 0 Mb of data
37:
37: Writing final coordinates.
37:
37: Core t (s) Wall t (s) (%)
37: Time: 0.350 0.175 199.8
37: (ns/day) (hour/ns)
37: Performance: 1.478 16.236
37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (299 ms)
37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (829 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 29 tests from 11 test cases ran. (14272 ms total)
37: [ PASSED ] 29 tests.
37/40 Test #37: MdrunTests ....................... Passed 14.35 sec
test 38
Start 38: MdrunNonIntegratorTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
38: Test timeout computed to be: 600
38: [==========] Running 57 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -4.79910464433648e+01
38: Maximum force = 1.86297359800823e+02 on atom 13
38: Norm of force = 8.77219867200409e+01
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1424 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 3.02331e+02 on atom 3
38: F-Norm = 1.18024e+02
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -5.58622539552396e+01
38: Maximum force = 4.27274823589569e+02 on atom 13
38: Norm of force = 1.84530029788183e+02
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1462 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 22.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 3.19376899489614e+02
38: Maximum force = 9.99884921027275e+03 on atom 9
38: Norm of force = 4.61669565061009e+03
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (489 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38:
38: NOTE 3 [file glycine_vacuo.top, line 12]:
38: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
38:
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 22.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 2.41575e+04 on atom 10
38: F-Norm = 1.18451e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 1.51743017875791e+02
38: Maximum force = 7.42089573427941e+03 on atom 9
38: Norm of force = 3.56929298621805e+03
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (507 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 3 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -1.56984194095142e+02
38: Maximum force = 4.56923625858570e+02 on atom 17
38: Norm of force = 1.83258377483232e+02
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (88 ms)
38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 3 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38:
38: NOTE 4 [file unknown]:
38: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 1.06800e+03 on atom 28
38: F-Norm = 4.26922e+02
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = -1.69410778941237e+02
38: Maximum force = 2.18225948179336e+02 on atom 17
38: Norm of force = 7.92068036007829e+01
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
38: This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (108 ms)
38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4079 ms total)
38:
38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents converged to Fmax < 10 in 1 steps
38: Potential Energy = -9.74257075835450e-01
38: Maximum force = 4.01322929015108e+00 on atom 1
38: Norm of force = 1.63839399694368e+00
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (56 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 4.01323e+00 on atom 1
38: F-Norm = 1.63839e+00
38:
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
38: Potential Energy = -9.90642313893957e-01
38: Maximum force = 2.57812909491105e+00 on atom 1
38: Norm of force = 1.05251679559258e+00
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (48 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 2 notes
38:
38: There was 1 warning
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Low-Memory BFGS Minimizer:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: Using 10 BFGS correction steps.
38:
38: F-max = 4.01323e+00 on atom 1
38: F-Norm = 1.63839e+00
38:
38:
38: writing lowest energy coordinates.
38:
38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
38: Potential Energy = -9.90642313893957e-01
38: Maximum force = 2.57812909491105e+00 on atom 1
38: Norm of force = 1.05251679559258e+00
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (48 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Steepest Descents:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Steepest Descents did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 3.19395484629890e+02
38: Maximum force = 9.97041707215792e+03 on atom 9
38: Norm of force = 4.62274878672162e+03
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (501 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Polak-Ribiere Conjugate Gradients:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: F-max = 2.41672e+04 on atom 10
38: F-Norm = 1.19357e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 1.56258793634223e+02
38: Maximum force = 7.50181017498406e+03 on atom 9
38: Norm of force = 3.61390332570589e+03
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (535 ms)
38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
38:
38: Generated 20503 of the 20503 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 1
38: Generated 17396 of the 20503 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Glycine'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 3 notes
38:
38: There was 1 warning
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38:
38: Low-Memory BFGS Minimizer:
38: Tolerance (Fmax) = 1.00000e+01
38: Number of steps = 4
38: Using 10 BFGS correction steps.
38:
38: F-max = 2.41672e+04 on atom 10
38: F-Norm = 1.19357e+04
38:
38:
38: Energy minimization reached the maximum number of steps before the forces
38: reached the requested precision Fmax < 10.
38:
38: writing lowest energy coordinates.
38:
38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
38: Potential Energy = 5.61116097533073e+02
38: Maximum force = 1.26854826292496e+04 on atom 10
38: Norm of force = 6.06436286981171e+03
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (533 ms)
38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1722 ms total)
38:
38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
38: NVE simulation: will use the initial temperature of 68.810 K for
38: determining the Verlet buffer size
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.477 0.238 199.9
38: (ns/day) (hour/ns)
38: Performance: 6.159 3.897
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr'
38:
38: trr version: GMX_trn_file (double precision)
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.003 195.7
38: (ns/day) (hour/ns)
38: Performance: 429.100 0.056
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (330 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
38: NVE simulation: will use the initial temperature of 68.810 K for
38: determining the Verlet buffer size
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.396 0.198 199.8
38: (ns/day) (hour/ns)
38: Performance: 7.414 3.237
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.008 0.004 195.9
38: (ns/day) (hour/ns)
38: Performance: 373.981 0.064
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (287 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.331 0.166 199.8
38: (ns/day) (hour/ns)
38: Performance: 8.869 2.706
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.009 0.005 196.1
38: (ns/day) (hour/ns)
38: Performance: 318.426 0.075
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (261 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 1 of the 1 non-bonded parameter combinations
38: Excluding 1 bonded neighbours molecule type 'Argon'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 33.00
38:
38: There were 3 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Argon'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.505 0.253 199.9
38: (ns/day) (hour/ns)
38: Performance: 5.816 4.126
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.006 0.003 195.9
38: (ns/day) (hour/ns)
38: Performance: 459.403 0.052
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (345 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: NVE simulation: will use the initial temperature of 398.997 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 1.157 0.578 199.9
38: (ns/day) (hour/ns)
38: Performance: 2.539 9.452
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.8
38: (ns/day) (hour/ns)
38: Performance: 386.923 0.062
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (2073 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: NVE simulation: will use the initial temperature of 398.997 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.426 0.213 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.893 3.482
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.7
38: (ns/day) (hour/ns)
38: Performance: 392.419 0.061
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (1767 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.441 0.221 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.653 3.607
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.008 0.004 196.2
38: (ns/day) (hour/ns)
38: Performance: 342.674 0.070
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (1746 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 330891 of the 330891 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 330891 of the 330891 1-4 parameter combinations
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 27.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'spc2'
38: 16 steps, 0.0 ps.
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.439 0.219 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.692 3.587
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.007 0.004 195.6
38: (ns/day) (hour/ns)
38: Performance: 384.460 0.062
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (1752 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: NVE simulation: will use the initial temperature of 456.887 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 7 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 7 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.503 0.252 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.834 4.114
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.011 0.005 197.2
38: (ns/day) (hour/ns)
38: Performance: 274.048 0.088
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (421 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: NVE simulation: will use the initial temperature of 456.887 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 7 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 7 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.479 0.240 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.131 3.914
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 197.1
38: (ns/day) (hour/ns)
38: Performance: 238.109 0.101
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (409 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 6 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.360 0.180 199.7
38: (ns/day) (hour/ns)
38: Performance: 8.151 2.945
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.010 0.005 197.1
38: (ns/day) (hour/ns)
38: Performance: 290.211 0.083
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (445 ms)
38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2145 of the 2145 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2145 of the 2145 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
38:
38: NOTE 4 [file unknown]:
38: You are using constraints on all bonds, whereas the forcefield has been
38: parametrized only with constraints involving hydrogen atoms. We suggest
38: using constraints = h-bonds instead, this will also improve performance.
38:
38: Cleaning up constraints and constant bonded interactions with virtual sites
38: Removed 18 Angles with virtual sites, 21 left
38: Removed 10 Proper Dih.s with virtual sites, 44 left
38: Converted 15 Constraints with virtual sites to connections, 7 left
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 23.00
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: There are 9 non-linear virtual site constructions. Their contribution to
38: the energy error is approximated. In most cases this does not affect the
38: error significantly.
38:
38:
38: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 6 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun 'Alanine dipeptide in vacuo'
38: 16 steps, 0.0 ps.
38: turning all bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.420 0.210 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.993 3.432
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.006 197.2
38: (ns/day) (hour/ns)
38: Performance: 230.311 0.104
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (469 ms)
38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (10309 ms total)
38:
38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.552 0.276 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.315 4.516
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.3
38: (ns/day) (hour/ns)
38: Performance: 185.075 0.130
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (476 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.452 0.227 199.6
38: (ns/day) (hour/ns)
38: Performance: 6.483 3.702
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.2
38: (ns/day) (hour/ns)
38: Performance: 185.890 0.129
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (399 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.470 0.235 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.245 3.843
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 192.0
38: (ns/day) (hour/ns)
38: Performance: 229.839 0.104
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (415 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.502 0.252 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.840 4.110
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.016 0.008 192.4
38: (ns/day) (hour/ns)
38: Performance: 180.731 0.133
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (429 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.471 0.236 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.225 3.855
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 189.8
38: (ns/day) (hour/ns)
38: Performance: 220.667 0.109
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (437 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.457 0.229 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.419 3.739
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.5
38: (ns/day) (hour/ns)
38: Performance: 183.340 0.131
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (397 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.503 0.252 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.832 4.115
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.018 0.009 192.2
38: (ns/day) (hour/ns)
38: Performance: 155.378 0.154
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (454 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.476 0.238 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.163 3.894
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 191.9
38: (ns/day) (hour/ns)
38: Performance: 188.346 0.127
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (418 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.475 0.238 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.177 3.885
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 191.2
38: (ns/day) (hour/ns)
38: Performance: 214.760 0.112
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (409 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.500 0.251 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.862 4.094
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 189.7
38: (ns/day) (hour/ns)
38: Performance: 181.008 0.133
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (439 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.508 0.254 199.6
38: (ns/day) (hour/ns)
38: Performance: 5.778 4.154
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.1
38: (ns/day) (hour/ns)
38: Performance: 185.086 0.130
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (442 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.578 0.289 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.080 4.725
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.4
38: (ns/day) (hour/ns)
38: Performance: 184.003 0.130
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (470 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.472 0.236 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.213 3.863
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.016 0.008 192.5
38: (ns/day) (hour/ns)
38: Performance: 180.954 0.133
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (420 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.501 0.251 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.853 4.101
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 192.2
38: (ns/day) (hour/ns)
38: Performance: 227.841 0.105
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (404 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.568 0.284 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.170 4.642
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.019 0.010 190.8
38: (ns/day) (hour/ns)
38: Performance: 147.112 0.163
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (481 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.503 0.252 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.835 4.113
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.016 0.009 192.1
38: (ns/day) (hour/ns)
38: Performance: 171.104 0.140
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (440 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.518 0.259 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.662 4.239
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.017 0.009 193.1
38: (ns/day) (hour/ns)
38: Performance: 167.385 0.143
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (445 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.490 0.246 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.980 4.013
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.016 0.008 192.7
38: (ns/day) (hour/ns)
38: Performance: 177.528 0.135
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (415 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.470 0.235 199.8
38: (ns/day) (hour/ns)
38: Performance: 6.240 3.846
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 192.6
38: (ns/day) (hour/ns)
38: Performance: 214.185 0.112
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (392 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.520 0.260 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.646 4.251
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.013 0.007 189.8
38: (ns/day) (hour/ns)
38: Performance: 219.566 0.109
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (431 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.569 0.285 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.159 4.652
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.4
38: (ns/day) (hour/ns)
38: Performance: 185.387 0.129
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (460 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: NVE simulation: will use the initial temperature of 293.480 K for
38: determining the Verlet buffer size
38:
38:
38: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 5 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.516 0.258 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.686 4.221
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.3 (double precision)
38: Can not increase nstlist because an NVE ensemble is used
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.018 0.009 192.6
38: (ns/day) (hour/ns)
38: Performance: 155.602 0.154
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (461 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.480 0.241 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.106 3.930
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.5
38: (ns/day) (hour/ns)
38: Performance: 185.409 0.129
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (498 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.545 0.273 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.387 4.455
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.016 0.008 192.6
38: (ns/day) (hour/ns)
38: Performance: 179.940 0.133
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (540 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.494 0.247 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.938 4.042
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.019 0.010 190.3
38: (ns/day) (hour/ns)
38: Performance: 150.240 0.160
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (512 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.527 0.264 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.562 4.315
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.2
38: (ns/day) (hour/ns)
38: Performance: 185.515 0.129
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (517 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.465 0.233 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.301 3.809
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.016 0.008 192.4
38: (ns/day) (hour/ns)
38: Performance: 181.029 0.133
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (491 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.535 0.268 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.487 4.374
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 192.0
38: (ns/day) (hour/ns)
38: Performance: 190.013 0.126
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (519 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.498 0.249 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.891 4.074
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 192.3
38: (ns/day) (hour/ns)
38: Performance: 232.871 0.103
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (514 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.517 0.259 199.8
38: (ns/day) (hour/ns)
38: Performance: 5.676 4.229
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.015 0.008 190.1
38: (ns/day) (hour/ns)
38: Performance: 184.504 0.130
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (493 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.461 0.231 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.362 3.772
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 192.2
38: (ns/day) (hour/ns)
38: Performance: 230.803 0.104
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (477 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.471 0.236 199.7
38: (ns/day) (hour/ns)
38: Performance: 6.231 3.852
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.012 0.006 192.3
38: (ns/day) (hour/ns)
38: Performance: 231.167 0.104
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (470 ms)
38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
38:
38: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]:
38: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
38: scheme was introduced, but the group scheme was still the default. The
38: default is now the Verlet scheme, so you will observe different behaviour.
38:
38:
38: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
38: that with the Verlet scheme, nstlist has no effect on the accuracy of
38: your simulation.
38:
38:
38: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: Setting nstcalcenergy (100) equal to nstenergy (4)
38:
38: Generated 2485 of the 2485 non-bonded parameter combinations
38: Generating 1-4 interactions: fudge = 0.5
38: Generated 2485 of the 2485 1-4 parameter combinations
38: Excluding 3 bonded neighbours molecule type 'nonanol'
38: Excluding 2 bonded neighbours molecule type 'SOL'
38: Removing all charge groups because cutoff-scheme=Verlet
38: Number of degrees of freedom in T-Coupling group System is 79.00
38:
38: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
38: You are using a plain Coulomb cut-off, which might produce artifacts.
38: You might want to consider using PME electrostatics.
38:
38:
38:
38: There were 4 notes
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting mdrun '30 system in water'
38: 16 steps, 0.0 ps.
38: turning H bonds into constraints...
38: turning H bonds into constraints...
38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
38: Note that mdrun will redetermine rlist based on the actual pair-list setup
38: This run will generate roughly 0 Mb of data
38:
38: Writing final coordinates.
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.499 0.250 199.7
38: (ns/day) (hour/ns)
38: Performance: 5.879 4.082
38: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
38: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.3 (double precision)
38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
38:
38: Using 1 MPI thread
38: Using 2 OpenMP threads
38:
38:
38: NOTE: The number of threads is not equal to the number of (logical) cores
38: and the -pin option is set to auto: will not pin threads to cores.
38: This can lead to significant performance degradation.
38: Consider using -pin on (and -pinoffset in case you run multiple jobs).
38:
38: WARNING: Using the slow plain C kernels. This should
38: not happen during routine usage on supported platforms.
38: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr'
38:
38:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
38:
38: Core t (s) Wall t (s) (%)
38: Time: 0.018 0.009 192.6
38: (ns/day) (hour/ns)
38: Performance: 157.996 0.152
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as double precision energy file
38: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as double precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
38:
38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (529 ms)
38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (15102 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 57 tests from 4 test cases ran. (31212 ms total)
38: [ PASSED ] 57 tests.
38/40 Test #38: MdrunNonIntegratorTests .......... Passed 31.37 sec
test 39
Start 39: LegacyGroupSchemeMdrunTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/legacy-mdrun-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml"
39: Test timeout computed to be: 600
39: [==========] Running 2 tests from 1 test case.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from Simple/TpiTest
39: [ RUN ] Simple/TpiTest.ReproducesOutput/0
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]:
39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
39: removed in a future release when all interaction forms are supported for
39: the verlet scheme. The verlet scheme already scales better, and it is
39: compatible with GPUs and other accelerators.
39:
39: Generated 331705 of the 331705 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 331705 of the 331705 1-4 parameter combinations
39: Excluding 2 bonded neighbours molecule type 'SOL'
39: Excluding 3 bonded neighbours molecule type 'methane'
39: Number of degrees of freedom in T-Coupling group System is 1308.00
39:
39: There was 1 note
39: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.3 (double precision)
39: Using 1 MPI thread
39:
39:
39: NOTE: Thread affinity was not set.
39:
39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
39: removed in a future release when 'verlet' supports all interaction forms.
39:
39: Reading frames from gro file '216 water molecules', 648 atoms.
39:
Reading frame 0 time 0.000 mu 8.698e+02 <mu> 8.698e+02
39:
Last frame 0 time 0.000
39: Analysing residue names:
39: There are: 216 Water residues
39: There are: 1 Other residues
39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm
39: Largest charge group radii for Coulomb: 0.100, 0.100 nm
39: This run will generate roughly 0 Mb of data
39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (1570 ms)
39: [ RUN ] Simple/TpiTest.ReproducesOutput/1
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]:
39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be
39: removed in a future release when all interaction forms are supported for
39: the verlet scheme. The verlet scheme already scales better, and it is
39: compatible with GPUs and other accelerators.
39:
39: Generated 331705 of the 331705 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 331705 of the 331705 1-4 parameter combinations
39: Excluding 2 bonded neighbours molecule type 'SOL'
39: Excluding 3 bonded neighbours molecule type 'methane'
39: Number of degrees of freedom in T-Coupling group System is 1308.00
39:
39: There was 1 note
39: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.3 (double precision)
39: Using 1 MPI thread
39:
39:
39: NOTE: Thread affinity was not set.
39:
39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be
39: removed in a future release when 'verlet' supports all interaction forms.
39:
39: Reading frames from gro file '216 water molecules', 648 atoms.
39:
Reading frame 0 time 0.000 mu 9.151e+01 <mu> 9.151e+01
39:
Last frame 0 time 0.000
39: Analysing residue names:
39: There are: 216 Water residues
39: There are: 1 Other residues
39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm
39: Largest charge group radii for Coulomb: 0.100, 0.100 nm
39: This run will generate roughly 0 Mb of data
39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (1488 ms)
39: [----------] 2 tests from Simple/TpiTest (3058 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 2 tests from 1 test case ran. (3058 ms total)
39: [ PASSED ] 2 tests.
39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 3.10 sec
test 40
Start 40: MdrunMpiTests
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
40: Test timeout computed to be: 600
40: [==========] Running 21 tests from 7 test cases.
40: [----------] Global test environment set-up.
40: [----------] 1 test from DomainDecompositionSpecialCasesTest
40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 806312958
40: Generated 3 of the 3 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 3 of the 3 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 9.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc2'
40: 0 steps, 0.0 ps.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.002 0.001 174.8
40: (ns/day) (hour/ns)
40: Performance: 63.355 0.379
40: This run will generate roughly 0 Mb of data
40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (58 ms)
40: [----------] 1 test from DomainDecompositionSpecialCasesTest (59 ms total)
40:
40: [----------] 4 tests from MimicTest
40: [ RUN ] MimicTest.OneQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -260046866
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.005 0.003 195.3
40: (ns/day) (hour/ns)
40: Performance: 33.062 0.726
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.OneQuantumMol (51 ms)
40: [ RUN ] MimicTest.AllQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 1051759548
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.005 0.003 195.4
40: (ns/day) (hour/ns)
40: Performance: 31.370 0.765
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.AllQuantumMol (49 ms)
40: [ RUN ] MimicTest.TwoQuantumMol
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -481051361
40: Generated 10 of the 10 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 10 of the 10 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 21.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: NVE simulation with an initial temperature of zero: will use a Verlet
40: buffer of 10%. Check your energy drift!
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/4water.gro'
40:
40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.008 0.004 196.7
40: (ns/day) (hour/ns)
40: Performance: 22.258 1.078
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.TwoQuantumMol (49 ms)
40: [ RUN ] MimicTest.BondCuts
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to 631437567
40: Generated 2211 of the 2211 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2211 of the 2211 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 66.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: NVE simulation: will use the initial temperature of 300.368 K for
40: determining the Verlet buffer size
40:
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/programs/mdrun/tests/ala.gro'
40:
40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
40:
Reading frame 0 time 0.000
Last frame 0 time 0.000
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.004 0.002 194.5
40: (ns/day) (hour/ns)
40: Performance: 43.661 0.550
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: This run will generate roughly 0 Mb of data
40: [ OK ] MimicTest.BondCuts (88 ms)
40: [----------] 4 tests from MimicTest (237 ms total)
40:
40: [----------] 1 test from MultiSimTerminationTest
40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
40: [----------] 1 test from MultiSimTerminationTest (0 ms total)
40:
40: [----------] 2 tests from PmeTest
40: [ RUN ] PmeTest.ReproducesEnergies
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40: Setting the LD random seed to -589393294
40: Generated 279 of the 1225 non-bonded parameter combinations
40: Excluding 2 bonded neighbours molecule type 'Methanol'
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group rest is 12.00
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
40: NVE simulation: will use the initial temperature of 1046.791 K for
40: determining the Verlet buffer size
40:
40: Estimate for the relative computational load of the PME mesh part: 1.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
40: The optimal PME mesh load for parallel simulations is below 0.5
40: and for highly parallel simulations between 0.25 and 0.33,
40: for higher performance, increase the cut-off and the PME grid spacing.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: Calculating fourier grid dimensions for X Y Z
40: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
40: This run will generate roughly 0 Mb of data
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.540 0.270 199.8
40: (ns/day) (hour/ns)
40: Performance: 6.713 3.575
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.523 0.262 199.9
40: (ns/day) (hour/ns)
40: Performance: 6.929 3.463
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
40: starting mdrun 'spc-and-methanol'
40: 20 steps, 0.0 ps.
40:
40: Writing final coordinates.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.499 0.250 199.9
40: (ns/day) (hour/ns)
40: Performance: 7.264 3.304
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1022 ms)
40: [ RUN ] PmeTest.ScalesTheBox
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: For a correct single-point energy evaluation with nsteps = 0, use
40: continuation = yes to avoid constraining the input coordinates.
40:
40: Setting the LD random seed to -821663483
40: Generated 279 of the 1225 non-bonded parameter combinations
40: Excluding 2 bonded neighbours molecule type 'Methanol'
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Searching the wall atom type(s)
40: Number of degrees of freedom in T-Coupling group rest is 13.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: NVE simulation: will use the initial temperature of 966.269 K for
40: determining the Verlet buffer size
40:
40: Estimate for the relative computational load of the PME mesh part: 1.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
40: The optimal PME mesh load for parallel simulations is below 0.5
40: and for highly parallel simulations between 0.25 and 0.33,
40: for higher performance, increase the cut-off and the PME grid spacing.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.3 (double precision)
40: Can not increase nstlist because an NVE ensemble is used
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40: starting mdrun 'spc-and-methanol'
40: 0 steps, 0.0 ps.
40:
40: Core t (s) Wall t (s) (%)
40: Time: 0.045 0.023 197.6
40: (ns/day) (hour/ns)
40: Performance: 3.807 6.305
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.269 K
40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
40: Note that mdrun will redetermine rlist based on the actual pair-list setup
40: Calculating fourier grid dimensions for X Y Z
40: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
40: This run will generate roughly 0 Mb of data
40: [ OK ] PmeTest.ScalesTheBox (238 ms)
40: [----------] 2 tests from PmeTest (1260 ms total)
40:
40: [----------] 1 test from ReplicaExchangeTerminationTest
40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
40:
40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -4.79910464433648e+01
40: Maximum force = 1.86297359800823e+02 on atom 13
40: Norm of force = 8.77219867200409e+01
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (1461 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 330891 of the 330891 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 330891 of the 330891 1-4 parameter combinations
40: Excluding 2 bonded neighbours molecule type 'SOL'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 3.02331e+02 on atom 3
40: F-Norm = 1.18024e+02
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -5.58622539552396e+01
40: Maximum force = 4.27274823589569e+02 on atom 13
40: Norm of force = 1.84530029788183e+02
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (1426 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 22.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 3.19376899489614e+02
40: Maximum force = 9.99884921027275e+03 on atom 9
40: Norm of force = 4.61669565061009e+03
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (493 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40:
40: NOTE 3 [file glycine_vacuo.top, line 12]:
40: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
40:
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 22.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 2.41575e+04 on atom 10
40: F-Norm = 1.18451e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 1.51743017875791e+02
40: Maximum force = 7.42089573427941e+03 on atom 9
40: Norm of force = 3.56929298621805e+03
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (510 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 2145 of the 2145 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2145 of the 2145 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
40:
40: NOTE 3 [file unknown]:
40: You are using constraints on all bonds, whereas the forcefield has been
40: parametrized only with constraints involving hydrogen atoms. We suggest
40: using constraints = h-bonds instead, this will also improve performance.
40:
40: Cleaning up constraints and constant bonded interactions with virtual sites
40: Removed 18 Angles with virtual sites, 21 left
40: Removed 10 Proper Dih.s with virtual sites, 44 left
40: Converted 15 Constraints with virtual sites to connections, 7 left
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 23.00
40:
40: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 4 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -1.56984194095142e+02
40: Maximum force = 4.56923625858570e+02 on atom 17
40: Norm of force = 1.83258377483232e+02
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (81 ms)
40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 2145 of the 2145 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 0.5
40: Generated 2145 of the 2145 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
40:
40: NOTE 3 [file unknown]:
40: You are using constraints on all bonds, whereas the forcefield has been
40: parametrized only with constraints involving hydrogen atoms. We suggest
40: using constraints = h-bonds instead, this will also improve performance.
40:
40:
40: NOTE 4 [file unknown]:
40: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
40:
40: Cleaning up constraints and constant bonded interactions with virtual sites
40: Removed 18 Angles with virtual sites, 21 left
40: Removed 10 Proper Dih.s with virtual sites, 44 left
40: Converted 15 Constraints with virtual sites to connections, 7 left
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 23.00
40:
40: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 5 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 1.06800e+03 on atom 28
40: F-Norm = 4.26922e+02
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = -1.69410778941237e+02
40: Maximum force = 2.18225948179336e+02 on atom 17
40: Norm of force = 7.92068036007829e+01
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
40: This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (82 ms)
40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (4054 ms total)
40:
40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents converged to Fmax < 10 in 1 steps
40: Potential Energy = -9.74257075835450e-01
40: Maximum force = 4.01322929015108e+00 on atom 1
40: Norm of force = 1.63839399694368e+00
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (25 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 4.01323e+00 on atom 1
40: F-Norm = 1.63839e+00
40:
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
40: Potential Energy = -9.90642313893957e-01
40: Maximum force = 2.57812909491105e+00 on atom 1
40: Norm of force = 1.05251679559258e+00
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (27 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40:
40: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
40:
40: Generated 1 of the 1 non-bonded parameter combinations
40: Excluding 1 bonded neighbours molecule type 'Argon'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 33.00
40:
40: There were 2 notes
40:
40: There was 1 warning
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.3 (double precision)
40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
40:
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Low-Memory BFGS Minimizer:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: Using 10 BFGS correction steps.
40:
40: F-max = 4.01323e+00 on atom 1
40: F-Norm = 1.63839e+00
40:
40:
40: writing lowest energy coordinates.
40:
40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
40: Potential Energy = -9.90642313893957e-01
40: Maximum force = 2.57812909491105e+00 on atom 1
40: Norm of force = 1.05251679559258e+00
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Steepest Descents:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Steepest Descents did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 3.19395484629890e+02
40: Maximum force = 9.97041707215792e+03 on atom 9
40: Norm of force = 4.62274878672162e+03
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (474 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.3 (double precision)
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Polak-Ribiere Conjugate Gradients:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: F-max = 2.41672e+04 on atom 10
40: F-Norm = 1.19357e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 1.56258793634223e+02
40: Maximum force = 7.50181017498406e+03 on atom 9
40: Norm of force = 3.61390332570589e+03
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (502 ms)
40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
40:
40: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]:
40: /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it
40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet
40: scheme was introduced, but the group scheme was still the default. The
40: default is now the Verlet scheme, so you will observe different behaviour.
40:
40:
40: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
40: that with the Verlet scheme, nstlist has no effect on the accuracy of
40: your simulation.
40:
40:
40: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
40:
40: Generated 20503 of the 20503 non-bonded parameter combinations
40: Generating 1-4 interactions: fudge = 1
40: Generated 17396 of the 20503 1-4 parameter combinations
40: Excluding 3 bonded neighbours molecule type 'Glycine'
40: Removing all charge groups because cutoff-scheme=Verlet
40: Number of degrees of freedom in T-Coupling group System is 27.00
40:
40: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
40: You are using a plain Coulomb cut-off, which might produce artifacts.
40: You might want to consider using PME electrostatics.
40:
40:
40:
40: There were 3 notes
40:
40: There was 1 warning
40: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
40: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.3 (double precision)
40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
40:
40: Using 1 MPI thread
40: Using 2 OpenMP threads
40:
40:
40: NOTE: The number of threads is not equal to the number of (logical) cores
40: and the -pin option is set to auto: will not pin threads to cores.
40: This can lead to significant performance degradation.
40: Consider using -pin on (and -pinoffset in case you run multiple jobs).
40:
40: WARNING: Using the slow plain C kernels. This should
40: not happen during routine usage on supported platforms.
40:
40: Low-Memory BFGS Minimizer:
40: Tolerance (Fmax) = 1.00000e+01
40: Number of steps = 4
40: Using 10 BFGS correction steps.
40:
40: F-max = 2.41672e+04 on atom 10
40: F-Norm = 1.19357e+04
40:
40:
40: Energy minimization reached the maximum number of steps before the forces
40: reached the requested precision Fmax < 10.
40:
40: writing lowest energy coordinates.
40:
40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
40: Potential Energy = 5.61116097533073e+02
40: Maximum force = 1.26854826292496e+04 on atom 10
40: Norm of force = 6.06436286981171e+03
40: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
40:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (474 ms)
40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (1525 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 21 tests from 7 test cases ran. (7138 ms total)
40: [ PASSED ] 21 tests.
40:
40: YOU HAVE 4 DISABLED TESTS
40:
40/40 Test #40: MdrunMpiTests .................... Passed 7.20 sec
100% tests passed, 0 tests failed out of 40
Label Time Summary:
GTest = 186.34 sec*proc (40 tests)
IntegrationTest = 56.35 sec*proc (5 tests)
MpiTest = 0.40 sec*proc (3 tests)
SlowTest = 111.05 sec*proc (1 test)
UnitTest = 18.94 sec*proc (34 tests)
Total Test time (real) = 186.68 sec
touch build-basic
dh_testdir
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make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
Scanning dependencies of target tng_io_obj
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/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
Scanning dependencies of target libgromacs_external
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target lmfit_objlib
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target libgromacs_external
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
"%4d-%02d-%02d %02d:%02d:%02d",
^~~~
In file included from /usr/include/stdio.h:873,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3243833 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
^
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
vectorSecondDerivative(ArrayRef<const double> f, double spacing)
^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/variant.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
updateForceCorrelationGrid(probWeightNeighbor, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tempForce_, biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleProbabilityWeights(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleCoordAndPmf(const Grid &grid,
^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
CoordState::sampleUmbrellaGridpoint(const Grid &grid,
^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void CorrelationTensor::addData(double weight,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSize(const BiasParams ¶ms,
^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/chargegroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation-utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ns.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/manage-threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/position-restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate-spline-moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald-utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long-range-correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-load-balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-pp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-solve.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spline-work.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program-impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/integrator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -P CMakeFiles/libgromacs.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
Scanning dependencies of target libgromacs_external
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
Scanning dependencies of target libgromacs_generated
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/programs /<<PKGBUILDDIR>>/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target libgromacs_external
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
"%4d-%02d-%02d %02d:%02d:%02d",
^~~~
In file included from /usr/include/stdio.h:873,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 27%] Built target libgromacs_generated
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3243833 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
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/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const MPI_Comm*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
static void low_set_ddbox(int numPbcDimensions,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void set_ddbox(const gmx_domdec_t &dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions,
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&dd.nc, box, calculateUnboundedSize, xRef,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddbox);
~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void set_ddbox_cr(const t_commrec &cr,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir),
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dd_nc, box, true, x, nullptr, ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void dd_collect_vec(gmx_domdec_t *dd,
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(const gmx_domdec_t *dd,
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, false, state.box, true, state.x, &ddbox);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog,
^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::LocalAtomSetManager*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog,
^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions,
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mtop, ir,
~~~~~~~~~
box, xGlobal,
~~~~~~~~~~~~~
&ddbox);
~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirForward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void dd_move_x(gmx_domdec_t *dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void dd_move_f(gmx_domdec_t *dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv(dd, d, dddirForward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
work.positionBuffer, rvecBufferRef);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
rvec *makeRvecArray(gmx::ArrayRef<const gmx::RVec> v,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, true,
~~~~~~~~~^~~~~~~~~~~
DDMASTER(dd) ? state_global->box : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
true, xGlobal,
~~~~~~~~~~~~~~
&ddbox);
~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, bMasterState, state_local->box,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
true, state_local->x, &ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, bMasterState, state_local->box,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bNStGlobalComm, state_local->x, &ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_local->x);
~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_local->x);
~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0,
~~
comm->zones.size[0].bb_x0,
~~~~~~~~~~~~~~~~~~~~~~~~~~
comm->zones.size[0].bb_x1,
~~~~~~~~~~~~~~~~~~~~~~~~~~
comm->updateGroupsCog.get(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, dd->ncg_home,
~~~~~~~~~~~~~~~~
comm->zones.dens_zone0,
~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo,
~~~~~~~~~~~
state_local->x,
~~~~~~~~~~~~~~~
ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->nbv->grp[eintLocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->nbv->nbat);
~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
vectorSecondDerivative(ArrayRef<const double> f, double spacing)
^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
^
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/variant.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:51:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx_bool, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
bool pullCheckPbcWithinGroup(const pull_t &pull,
^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
updateForceCorrelationGrid(probWeightNeighbor, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tempForce_, biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleProbabilityWeights(const Grid &grid,
^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleCoordAndPmf(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
CoordState::sampleUmbrellaGridpoint(const Grid &grid,
^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void CorrelationTensor::addData(double weight,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSize(const BiasParams ¶ms,
^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/chargegroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation-utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
BoxDeformation::apply(ArrayRef<RVec> x,
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void calc_mu(int start, int homenr, gmx::ArrayRef<gmx::RVec> x, const real q[], const real qB[],
^~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
static void constr_recur(const t_blocka *at2con,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
t_blocka make_at2con(const gmx_moltype_t &moltype,
^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const gmx_bool*, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void andersen_tcoupl(const t_inputrec *ir, int64_t step,
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda *fepvals)
^~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdsetup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(f_global), f_local.size()));
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void nbnxn_put_on_grid(nbnxn_search_t nbs,
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
zone, c0, c1,
~~~~~~~~~~~~~
nullptr,
~~~~~~~~
zones->cg_range[zone],
~~~~~~~~~~~~~~~~~~~~~~
zones->cg_range[zone+1],
~~~~~~~~~~~~~~~~~~~~~~~~
-1,
~~~
atinfo,
~~~~~~~
x,
~~
0, nullptr,
~~~~~~~~~~~
nb_kernel_type,
~~~~~~~~~~~~~~~
nbat);
~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ns.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
int add_binr(t_bin *b, gmx::ArrayRef<const real> r)
^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void extract_binr(t_bin *b, int index, gmx::ArrayRef<real> r)
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdstep, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceWithPadding[Min], force_vir, md, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1, nrnb, wcycle,
~~~~~~~~~~~~~~~~
top, groups, state->box, posWithPadding[Try], &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceWithPadding[Try], force_vir,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
md, enerd, fcd, state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shellfc_flags,
~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(FILE *fplog,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2119:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void do_force(FILE *fplog,
^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, vzero, box_diag,
~~~~~~~~~~~~~~~~~~~
nullptr, 0, mdatoms->homenr, -1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo, x.unpaddedArrayRef(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, nullptr,
~~~~~~~~~~~
nbv->grp[eintLocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->nbat);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd),
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo, x.unpaddedArrayRef(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->grp[eintNonlocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->nbat);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, wcycle,
~~~~~~~~~~~~~~~~
fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flags, &forceWithVirial, enerd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ed, bNS);
~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1626:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2047:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, wcycle,
~~~~~~~~~~~~~~~~
fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flags, &forceWithVirial, enerd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ed, bNS);
~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2058:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2069:26: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2721:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2874:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0)
^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(FILE *fplog,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, state, state_global, observablesHistory, f);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
^~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
upd->deform->apply(localX, state->box, step);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_update_t*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
andersen_tcoupl(ir, step, cr, md, v, rate,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
upd->sd->randomize_group, upd->sd->boltzfac);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wnblist.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/disre.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void constructVsitesGlobal(const gmx_mtop_t &mtop,
^~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/gpubonded-impl.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.3':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/manage-threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/position-restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate-spline-moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald-utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long-range-correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-load-balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-pp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-solve.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spline-work.cpp
/usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program-impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/integrator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
count, nrnb, wcycle, top, &top_global->groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_NS : 0),
~~~~~~~~~~~~~~~~~~~~~~~~~
DOMAINDECOMP(cr) ?
~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::yes :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::no,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DOMAINDECOMP(cr) ?
~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::yes :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::no);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:875:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_NS : 0) | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1026:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1051:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
checkpointHandler->isCheckpointingStep(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bRerunMD, bLastStep,
~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1089:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1292:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NS | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
isCheckpointingStep, doRerun, isLastStep,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<real>(step), &ems.s, state_global, observablesHistory, ems.f);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NS | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
isCheckpointingStep, doRerun, isLastStep,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state, flocal, ftemp);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mimicCommunicator.sendForces(ftemp, state_global->natoms);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, &top_global->groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_global->lambda,
~~~~~~~~~~~~~~~~~~~~~
nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bStateChanged ? GMX_FORCE_STATECHANGED : 0),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::no,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::no);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:922:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&mtop, inputrec,
~~~~~~~~~~~~~~~~
box, positionsFromStatePointer(globalState.get()),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&atomSets);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1278:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
constructVsitesGlobal(mtop, globalState->x);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/mdmodules.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
^~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -P CMakeFiles/libgromacs.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libgromacs_mdrun_mpi_d.mpich.a CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
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cd /<<PKGBUILDDIR>>/build/mpich/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
[ 22%] Built target libgromacs_generated
cd /<<PKGBUILDDIR>>/build/mpich/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 22%] Built target onlinehelp-test-shared
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 23%] Built target mdrunutility-test-shared
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
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[ 80%] Built target libgromacs
cd /<<PKGBUILDDIR>>/build/mpich/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o
/usr/bin/ranlib ../../../lib/libgmock.a
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[ 81%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/testutils /<<PKGBUILDDIR>>/build/mpich/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
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/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi-printer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata-xml.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils-mpi-test
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cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
Scanning dependencies of target testutils-test
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cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
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[ 83%] Built target testutils-mpi-test
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied-forces-test
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cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp
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cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed-forces-test
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/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 84%] Built target applied-forces-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 84%] Built target listed-forces-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 85%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 85%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 86%] Built target mdlib-test
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 87%] Built target commandline-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 88%] Built target fft-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 88%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 88%] Built target mdrunutility-mpi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 88%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 89%] Built target ewald-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 89%] Built target mdrunutility-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 90%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
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/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 91%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 91%] Built target math-test
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 92%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 92%] Built target table-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 93%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/bits/random.h:34,
from /usr/include/c++/8/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 94%] Built target options-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 94%] Built target pull-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 95%] Built target random-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
[ 95%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 95%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 97%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[100%] Built target utility-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
(cd build/mpich; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/mpich/lib \
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i armhf )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/mpich/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/mpich/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/mpich/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/mpich/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/mpich
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1/27 Test #1: TestUtilsUnitTests ...............***Exception: SegFault 0.14 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /usr/bin/mpiexec.mpich "-np" "2" "-host" "localhost" "/<<PKGBUILDDIR>>/build/mpich/bin/testutils-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2:
2: ===================================================================================
2: = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
2: = PID 6162 RUNNING AT localhost
2: = EXIT CODE: 11
2: = CLEANING UP REMAINING PROCESSES
2: = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
2: ===================================================================================
2: YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
2: This typically refers to a problem with your application.
2: Please see the FAQ page for debugging suggestions
2/27 Test #2: TestUtilsMpiUnitTests ............***Failed 0.18 sec
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 6162 RUNNING AT localhost
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3/27 Test #3: MdlibUnitTest ....................***Exception: SegFault 0.08 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4/27 Test #4: AppliedForcesUnitTest ............***Exception: SegFault 0.02 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5/27 Test #5: ListedForcesTest .................***Exception: SegFault 0.03 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6/27 Test #6: CommandLineUnitTests .............***Exception: SegFault 0.02 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7/27 Test #7: DomDecTests ......................***Exception: SegFault 0.02 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8/27 Test #8: EwaldUnitTests ...................***Exception: SegFault 0.05 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9/27 Test #9: FFTUnitTests .....................***Exception: SegFault 0.02 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10/27 Test #10: GpuUtilsUnitTests ................***Exception: SegFault 0.02 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11/27 Test #11: HardwareUnitTests ................***Exception: SegFault 0.02 sec
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12/27 Test #12: MathUnitTests ....................***Exception: SegFault 0.02 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13/27 Test #13: MdrunUtilityUnitTests ............***Exception: SegFault 0.02 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/mpich/bin/mdrunutility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14:
14: ===================================================================================
14: = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
14: = PID 6177 RUNNING AT localhost
14: = EXIT CODE: 11
14: = CLEANING UP REMAINING PROCESSES
14: = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
14: ===================================================================================
14: YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
14: This typically refers to a problem with your application.
14: Please see the FAQ page for debugging suggestions
14/27 Test #14: MdrunUtilityMpiUnitTests .........***Failed 0.08 sec
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 6177 RUNNING AT localhost
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15/27 Test #15: OnlineHelpUnitTests ..............***Exception: SegFault 0.03 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16/27 Test #16: OptionsUnitTests .................***Exception: SegFault 0.03 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17/27 Test #17: RandomUnitTests ..................***Exception: SegFault 0.06 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18/27 Test #18: RestraintTests ...................***Exception: SegFault 0.02 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19/27 Test #19: TableUnitTests ...................***Exception: SegFault 0.02 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20/27 Test #20: TaskAssignmentUnitTests ..........***Exception: SegFault 0.02 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21/27 Test #21: UtilityUnitTests .................***Exception: SegFault 0.03 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/mpich/bin/utility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22:
22: ===================================================================================
22: = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
22: = PID 6190 RUNNING AT localhost
22: = EXIT CODE: 11
22: = CLEANING UP REMAINING PROCESSES
22: = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
22: ===================================================================================
22: YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
22: This typically refers to a problem with your application.
22: Please see the FAQ page for debugging suggestions
22/27 Test #22: UtilityMpiUnitTests ..............***Failed 0.07 sec
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 6190 RUNNING AT localhost
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23/27 Test #23: FileIOTests ......................***Exception: SegFault 0.03 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24/27 Test #24: PullTest .........................***Exception: SegFault 0.03 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25/27 Test #25: AwhTest ..........................***Exception: SegFault 0.03 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26/27 Test #26: SimdUnitTests ....................***Exception: SegFault 0.02 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/mpich/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27/27 Test #27: CompatibilityHelpersTests ........***Exception: SegFault 0.02 sec
0% tests passed, 27 tests failed out of 27
Label Time Summary:
GTest = 1.14 sec*proc (27 tests)
MpiTest = 0.33 sec*proc (3 tests)
UnitTest = 1.14 sec*proc (27 tests)
Total Test time (real) = 1.34 sec
The following tests FAILED:
1 - TestUtilsUnitTests (SEGFAULT)
2 - TestUtilsMpiUnitTests (Failed)
3 - MdlibUnitTest (SEGFAULT)
4 - AppliedForcesUnitTest (SEGFAULT)
5 - ListedForcesTest (SEGFAULT)
6 - CommandLineUnitTests (SEGFAULT)
7 - DomDecTests (SEGFAULT)
8 - EwaldUnitTests (SEGFAULT)
9 - FFTUnitTests (SEGFAULT)
10 - GpuUtilsUnitTests (SEGFAULT)
11 - HardwareUnitTests (SEGFAULT)
12 - MathUnitTests (SEGFAULT)
13 - MdrunUtilityUnitTests (SEGFAULT)
14 - MdrunUtilityMpiUnitTests (Failed)
15 - OnlineHelpUnitTests (SEGFAULT)
16 - OptionsUnitTests (SEGFAULT)
17 - RandomUnitTests (SEGFAULT)
18 - RestraintTests (SEGFAULT)
19 - TableUnitTests (SEGFAULT)
20 - TaskAssignmentUnitTests (SEGFAULT)
21 - UtilityUnitTests (SEGFAULT)
22 - UtilityMpiUnitTests (Failed)
23 - FileIOTests (SEGFAULT)
24 - PullTest (SEGFAULT)
25 - AwhTest (SEGFAULT)
26 - SimdUnitTests (SEGFAULT)
27 - CompatibilityHelpersTests (SEGFAULT)
Errors while running CTest
/usr/bin/make -j4 -C build/mpich-dp tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles 99
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target lmfit_objlib
/usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend
[ 3%] Built target tng_io_obj
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/external/googletest /<<PKGBUILDDIR>>/build/mpich-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color=
[ 4%] Built target libgromacs_external
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build
Scanning dependencies of target onlinehelp-test-shared
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
Scanning dependencies of target gmock
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
[ 22%] Built target libgromacs_generated
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 22%] Built target onlinehelp-test-shared
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 23%] Built target mdrunutility-test-shared
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 80%] Built target libgromacs
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o
/usr/bin/ranlib ../../../lib/libgmock.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 81%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi-printer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata-xml.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
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Scanning dependencies of target compat-test
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Scanning dependencies of target testutils-test
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cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
[ 83%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied-forces-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 84%] Built target compat-test
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void {anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::SettleTest_SatisfiesConstraints_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 84%] Built target applied-forces-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 84%] Built target listed-forces-test
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 85%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 85%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
updateGroupsCog.addCogs(globalAtomIndices, positions);
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 86%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:97:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:165:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:174:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/map:61,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:47:
/usr/include/c++/8/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::map(std::initializer_list<std::pair<const _Key, _Tp> >, const _Compare&, const allocator_type&) [with _Key = gmx::BasicVector<int>; _Tp = t_complex; _Compare = std::less<gmx::BasicVector<int> >; _Alloc = std::allocator<std::pair<const gmx::BasicVector<int>, t_complex> >]':
/usr/include/c++/8/bits/stl_map.h:226:7: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
map(initializer_list<value_type> __l,
^~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 87%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 88%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
vector(_InputIterator __first, _InputIterator __last,
^~~~~~
/usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 88%] Built target hardware-test
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:326:114: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates1(c_sampleCoordinatesFull.begin(), c_sampleCoordinatesFull.begin() + 1);
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:118: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates2(c_sampleCoordinatesFull.begin() + 1, c_sampleCoordinatesFull.begin() + 3);
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:330:120: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates13(c_sampleCoordinatesFull.begin() + 3, c_sampleCoordinatesFull.begin() + 16);
^
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void runTest(const gmx_gpu_info_t &gpuInfo,
^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void runTest(const gmx_gpu_info_t &gpuInfo,
^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 88%] Built target gpu_utils-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
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/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
[ 89%] Built target ewald-test
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 89%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 89%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 90%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 91%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 91%] Built target math-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/bits/random.h:34,
from /usr/include/c++/8/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 91%] Built target table-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 92%] Built target random-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 93%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 94%] Built target utility-mpi-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 95%] Built target options-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 95%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 95%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/gmxregex.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 95%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 97%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[100%] Built target simd-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
(cd build/mpich-dp ; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/mpich-dp/lib \
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i armhf )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/mpich-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/mpich-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/mpich-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/mpich-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/mpich-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1/27 Test #1: TestUtilsUnitTests ...............***Exception: SegFault 0.06 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /usr/bin/mpiexec.mpich "-np" "2" "-host" "localhost" "/<<PKGBUILDDIR>>/build/mpich-dp/bin/testutils-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2:
2: ===================================================================================
2: = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
2: = PID 13610 RUNNING AT localhost
2: = EXIT CODE: 11
2: = CLEANING UP REMAINING PROCESSES
2: = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
2: ===================================================================================
2: YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
2: This typically refers to a problem with your application.
2: Please see the FAQ page for debugging suggestions
2/27 Test #2: TestUtilsMpiUnitTests ............***Failed 0.06 sec
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 13610 RUNNING AT localhost
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3/27 Test #3: MdlibUnitTest ....................***Exception: SegFault 0.04 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4/27 Test #4: AppliedForcesUnitTest ............***Exception: SegFault 0.03 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5/27 Test #5: ListedForcesTest .................***Exception: SegFault 0.03 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6/27 Test #6: CommandLineUnitTests .............***Exception: SegFault 0.02 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7/27 Test #7: DomDecTests ......................***Exception: SegFault 0.02 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8/27 Test #8: EwaldUnitTests ...................***Exception: SegFault 0.03 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9/27 Test #9: FFTUnitTests .....................***Exception: SegFault 0.02 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10/27 Test #10: GpuUtilsUnitTests ................***Exception: SegFault 0.03 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11/27 Test #11: HardwareUnitTests ................***Exception: SegFault 0.03 sec
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12/27 Test #12: MathUnitTests ....................***Exception: SegFault 0.03 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13/27 Test #13: MdrunUtilityUnitTests ............***Exception: SegFault 0.03 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/mpich-dp/bin/mdrunutility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14:
14: ===================================================================================
14: = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
14: = PID 13625 RUNNING AT localhost
14: = EXIT CODE: 11
14: = CLEANING UP REMAINING PROCESSES
14: = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
14: ===================================================================================
14: YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
14: This typically refers to a problem with your application.
14: Please see the FAQ page for debugging suggestions
14/27 Test #14: MdrunUtilityMpiUnitTests .........***Failed 0.07 sec
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 13625 RUNNING AT localhost
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15/27 Test #15: OnlineHelpUnitTests ..............***Exception: SegFault 0.03 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16/27 Test #16: OptionsUnitTests .................***Exception: SegFault 0.03 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17/27 Test #17: RandomUnitTests ..................***Exception: SegFault 0.06 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18/27 Test #18: RestraintTests ...................***Exception: SegFault 0.03 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19/27 Test #19: TableUnitTests ...................***Exception: SegFault 0.03 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20/27 Test #20: TaskAssignmentUnitTests ..........***Exception: SegFault 0.03 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21/27 Test #21: UtilityUnitTests .................***Exception: SegFault 0.04 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /usr/bin/mpiexec.mpich "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/mpich-dp/bin/utility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22:
22: ===================================================================================
22: = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
22: = PID 13638 RUNNING AT localhost
22: = EXIT CODE: 11
22: = CLEANING UP REMAINING PROCESSES
22: = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
22: ===================================================================================
22: YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
22: This typically refers to a problem with your application.
22: Please see the FAQ page for debugging suggestions
22/27 Test #22: UtilityMpiUnitTests ..............***Failed 0.08 sec
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 13638 RUNNING AT localhost
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23/27 Test #23: FileIOTests ......................***Exception: SegFault 0.03 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24/27 Test #24: PullTest .........................***Exception: SegFault 0.03 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25/27 Test #25: AwhTest ..........................***Exception: SegFault 0.02 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26/27 Test #26: SimdUnitTests ....................***Exception: SegFault 0.02 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/mpich-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/mpich-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27/27 Test #27: CompatibilityHelpersTests ........***Exception: SegFault 0.02 sec
0% tests passed, 27 tests failed out of 27
Label Time Summary:
GTest = 0.98 sec*proc (27 tests)
MpiTest = 0.21 sec*proc (3 tests)
UnitTest = 0.98 sec*proc (27 tests)
Total Test time (real) = 1.12 sec
The following tests FAILED:
1 - TestUtilsUnitTests (SEGFAULT)
2 - TestUtilsMpiUnitTests (Failed)
3 - MdlibUnitTest (SEGFAULT)
4 - AppliedForcesUnitTest (SEGFAULT)
5 - ListedForcesTest (SEGFAULT)
6 - CommandLineUnitTests (SEGFAULT)
7 - DomDecTests (SEGFAULT)
8 - EwaldUnitTests (SEGFAULT)
9 - FFTUnitTests (SEGFAULT)
10 - GpuUtilsUnitTests (SEGFAULT)
11 - HardwareUnitTests (SEGFAULT)
12 - MathUnitTests (SEGFAULT)
13 - MdrunUtilityUnitTests (SEGFAULT)
14 - MdrunUtilityMpiUnitTests (Failed)
15 - OnlineHelpUnitTests (SEGFAULT)
16 - OptionsUnitTests (SEGFAULT)
17 - RandomUnitTests (SEGFAULT)
18 - RestraintTests (SEGFAULT)
19 - TableUnitTests (SEGFAULT)
20 - TaskAssignmentUnitTests (SEGFAULT)
21 - UtilityUnitTests (SEGFAULT)
22 - UtilityMpiUnitTests (Failed)
23 - FileIOTests (SEGFAULT)
24 - PullTest (SEGFAULT)
25 - AwhTest (SEGFAULT)
26 - SimdUnitTests (SEGFAULT)
27 - CompatibilityHelpersTests (SEGFAULT)
Errors while running CTest
touch build-mpich
dh_testdir
/usr/bin/make -j4 -C build/openmpi
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/openmpi/CMakeFiles /<<PKGBUILDDIR>>/build/openmpi/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
Scanning dependencies of target libgromacs_external
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
Scanning dependencies of target libgromacs_generated
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 1%] Built target lmfit_objlib
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/programs /<<PKGBUILDDIR>>/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 1%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
[ 2%] Built target libgromacs_external
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
"%4d-%02d-%02d %02d:%02d:%02d",
^~~~
In file included from /usr/include/stdio.h:873,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/openmpi/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3243833 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
^
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
vectorSecondDerivative(ArrayRef<const double> f, double spacing)
^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/variant.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/variant.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
updateForceCorrelationGrid(probWeightNeighbor, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tempForce_, biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleProbabilityWeights(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleCoordAndPmf(const Grid &grid,
^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
CoordState::sampleUmbrellaGridpoint(const Grid &grid,
^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void CorrelationTensor::addData(double weight,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSize(const BiasParams ¶ms,
^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/chargegroup.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation-utilities.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_tuning.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ns.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/cmake -P CMakeFiles/libgromacs.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 1%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 2%] Built target libgromacs_external
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str':
/<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=]
"%4d-%02d-%02d %02d:%02d:%02d",
^~~~
In file included from /usr/include/stdio.h:873,
from /<<PKGBUILDDIR>>/src/external/tng_io/include/tng/tng_io.h:308,
from /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c:20:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24
return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/openmpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.3243833 -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, ompi_communicator_t* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:235:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
static void low_set_ddbox(int numPbcDimensions,
^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void set_ddbox(const gmx_domdec_t &dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
low_set_ddbox(dd.npbcdim, dd.numBoundedDimensions,
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&dd.nc, box, calculateUnboundedSize, xRef,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddbox);
~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:296:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:308:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void set_ddbox_cr(const t_commrec &cr,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:317:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir),
~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dd_nc, box, true, x, nullptr, ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void dd_collect_vec(gmx_domdec_t *dd,
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:310:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:315:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->v), globalVRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:320:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(dd, state_local, makeConstArrayRef(state_local->cg_p), globalCgpRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(const gmx_domdec_t *dd,
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:128:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const t_state&, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3015:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, false, state.box, true, state.x, &ddbox);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void set_dd_limits_and_grid(const gmx::MDLogger&, t_commrec*, gmx_domdec_t*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2137:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
static void set_dd_limits_and_grid(const gmx::MDLogger &mdlog,
^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2358:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox_cr(*cr, &dd->nc, *ir, box, xGlobal, ddbox);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2383:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox_cr(*cr, nullptr, *ir, box, xGlobal, ddbox);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_domdec_t* init_domain_decomposition(const gmx::MDLogger&, t_commrec*, const DomdecOptions&, const MdrunOptions&, const gmx_mtop_t*, const t_inputrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::LocalAtomSetManager*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2953:15: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
gmx_domdec_t *init_domain_decomposition(const gmx::MDLogger &mdlog,
^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2979:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_dd_limits_and_grid(mdlog, cr, dd, options, mdrunOptions,
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mtop, ir,
~~~~~~~~~
box, xGlobal,
~~~~~~~~~~~~~
&ddbox);
~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:598:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirForward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:664:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:296:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void dd_move_x(gmx_domdec_t *dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:386:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:408:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void dd_move_f(gmx_domdec_t *dd,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv(dd, d, dddirForward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
sendBuffer, receiveBuffer);
~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:472:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
ddSendrecv(dd, d, dddirBackward,
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:259:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
work.positionBuffer, rvecBufferRef);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2236:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:207:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
rvec *makeRvecArray(gmx::ArrayRef<const gmx::RVec> v,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t*, const t_inputrec*, t_state*, gmx::PaddedVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3244:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, true,
~~~~~~~~~^~~~~~~~~~~
DDMASTER(dd) ? state_global->box : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
true, xGlobal,
~~~~~~~~~~~~~~
&ddbox);
~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3297:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, bMasterState, state_local->box,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
true, state_local->x, &ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3316:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
set_ddbox(*dd, bMasterState, state_local->box,
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bNStGlobalComm, state_local->x, &ddbox);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_local->x);
~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3336:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
comm->updateGroupsCog->addCogs(gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_local->x);
~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3364:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3419:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(fr->nbv->nbs.get(), fr->ePBC, state_local->box,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0,
~~
comm->zones.size[0].bb_x0,
~~~~~~~~~~~~~~~~~~~~~~~~~~
comm->zones.size[0].bb_x1,
~~~~~~~~~~~~~~~~~~~~~~~~~~
comm->updateGroupsCog.get(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, dd->ncg_home,
~~~~~~~~~~~~~~~~
comm->zones.dens_zone0,
~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo,
~~~~~~~~~~~
state_local->x,
~~~~~~~~~~~~~~~
ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->nbv->grp[eintLocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->nbv->nbat);
~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc-simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc-simd.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1413:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1473:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1531:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:397:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:212:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:290:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:309:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
vectorSecondDerivative(ArrayRef<const double> f, double spacing)
^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:361:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:100: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
^
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio-xdr.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:51:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' {aka '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'void init_swapcoords(FILE*, t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const MdrunOptions&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' {aka '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx_bool, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:950:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
bool pullCheckPbcWithinGroup(const pull_t &pull,
^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/8/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, pull_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' {aka '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:378:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor,
^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:399:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:107:41: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
updateForceCorrelationGrid(probWeightNeighbor, t);
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tempForce_, biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:173:49: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
state_.calcUmbrellaForceAndPotential(dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor, biasForce_, step, seed, params_.biasIndex);
~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >'} changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:293:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
void updateTargetDistribution(gmx::ArrayRef<PointState> pointState,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:423:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::calcConvolvedForce(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:443:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
double BiasState::moveUmbrella(const std::vector<DimParams> &dimParams,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:474:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor, step, seed, indexSeed);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:483:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1231:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleProbabilityWeights(const Grid &grid,
^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void BiasState::sampleCoordAndPmf(const Grid &grid,
^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:131:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
CoordState::sampleUmbrellaGridpoint(const Grid &grid,
^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:226:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void CorrelationTensor::addData(double weight,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_, weightSumCovering_, fplog);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1074:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/read-params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read-params.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:78:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSizeInitialStage(const BiasParams ¶ms,
^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:210:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
double HistogramSize::newHistogramSize(const BiasParams ¶ms,
^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/chargegroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/chargegroup.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/conformation-utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation-utilities.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_generic_cg.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_generic_cg.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_kernel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_kernel.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nonbonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:109:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
BoxDeformation::apply(ArrayRef<RVec> x,
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void calc_mu(int start, int homenr, gmx::ArrayRef<gmx::RVec> x, const real q[], const real qB[],
^~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' {aka '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> get_verlet_buffer_atomtypes(const gmx_mtop_t*, bool, int*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/8/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
static void constr_recur(const t_blocka *at2con,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:848:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
t_blocka make_at2con(const gmx_moltype_t &moltype,
^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const gmx_bool*, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:781:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void andersen_tcoupl(const t_inputrec *ir, int64_t step,
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, t_lambda*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:698:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
void sum_dhdl(gmx_enerdata_t *enerd, gmx::ArrayRef<const real> lambda, t_lambda *fepvals)
^~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdsetup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, gmx_mtop_t*, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:247:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:269:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:274:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, makeArrayRef(state_local->v), globalVRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:280:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(f_global), f_local.size()));
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_atomdata.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid(nbnxn_search_t, int, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, int, int, real, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1416:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void nbnxn_put_on_grid(nbnxn_search_t nbs,
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nbnxn_search_t, const gmx_domdec_zones_t*, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1520:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void nbnxn_put_on_grid_nonlocal(nbnxn_search_t nbs,
^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_grid.cpp:1536:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
zone, c0, c1,
~~~~~~~~~~~~~
nullptr,
~~~~~~~~
zones->cg_range[zone],
~~~~~~~~~~~~~~~~~~~~~~
zones->cg_range[zone+1],
~~~~~~~~~~~~~~~~~~~~~~~~
-1,
~~~
atinfo,
~~~~~~~
x,
~~
0, nullptr,
~~~~~~~~~~~
nb_kernel_type,
~~~~~~~~~~~~~~~
nbat);
~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nbnxn_search.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
int add_binr(t_bin *b, gmx::ArrayRef<const real> r)
^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void extract_binr(t_bin *b, int index, gmx::ArrayRef<real> r)
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx_bool, int, gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, t_state*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, const gmx_groups_t*, gmx_shellfc_t*, t_forcerec*, gmx::PpForceWorkload*, double, real*, const gmx_vsite_t*, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1144:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdstep, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceWithPadding[Min], force_vir, md, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/shellfc.cpp:1254:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1, nrnb, wcycle,
~~~~~~~~~~~~~~~~
top, groups, state->box, posWithPadding[Try], &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
forceWithPadding[Try], force_vir,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
md, enerd, fcd, state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shellfc_flags,
~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void computeSpecialForces(FILE*, const t_commrec*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, double, gmx_wallcycle_t, ForceProviders*, real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, const t_mdatoms*, real*, int, gmx::ForceWithVirial*, gmx_enerdata_t*, gmx_edsam*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:796:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(FILE *fplog,
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, int64_t, t_nrnb*, gmx_wallcycle_t, gmx_localtop_t*, const gmx_groups_t*, real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::PpForceWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, DdOpenBalanceRegionBeforeForceComputation, DdCloseBalanceRegionAfterForceComputation)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2119:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void do_force(FILE *fplog,
^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1175:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid(nbv->nbs.get(), fr->ePBC, box,
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, vzero, box_diag,
~~~~~~~~~~~~~~~~~~~
nullptr, 0, mdatoms->homenr, -1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo, x.unpaddedArrayRef(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
0, nullptr,
~~~~~~~~~~~
nbv->grp[eintLocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->nbat);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
nbnxn_put_on_grid_nonlocal(nbv->nbs.get(), domdec_zones(cr->dd),
~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fr->cginfo, x.unpaddedArrayRef(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->grp[eintNonlocal].kernel_type,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nbv->nbat);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1187:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1575:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, wcycle,
~~~~~~~~~~~~~~~~
fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flags, &forceWithVirial, enerd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ed, bNS);
~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1626:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2047:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
computeSpecialForces(fplog, cr, inputrec, awh, enforcedRotation,
~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, wcycle,
~~~~~~~~~~~~~~~~
fr->forceProviders, box, x.unpaddedArrayRef(), mdatoms, lambda,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
flags, &forceWithVirial, enerd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ed, bNS);
~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2058:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, force.unpaddedArrayRef(), fr->fshift, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2069:26: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_move_f(cr->dd, forceWithVirial.force_, nullptr, wcycle);
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2721:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void initialize_lambdas(FILE*, t_inputrec*, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2874:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0)
^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_md(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, double*, double*, t_state*, double*, t_nrnb*, gmx_mtop_t*, gmx_update_t**, gmx::BoxDeformation*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, real (*)[3], real (*)[3], real (*)[3], real (*)[3], real*, gmx_bool*, t_vcm**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2972:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:2978:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void init_rerun(FILE*, const t_commrec*, gmx::IMDOutputProvider*, t_inputrec*, const gmx_output_env_t*, const MdrunOptions&, t_state*, double*, t_nrnb*, gmx_mtop_t*, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &globalState->fep_state, globalState->lambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3046:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &tmpFepState, tmpLambda, lam0);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:3052:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, t_mdebin*, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:57:1: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(FILE *fplog,
^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:164:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, t, state, state_global, observablesHistory, f);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:85:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
^~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], t_state*, t_nrnb*, gmx_update_t*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1781:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
upd->deform->apply(localX, state->box, step);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx_update_t*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1920:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
extern gmx_bool update_randomize_velocities(const t_inputrec *ir, int64_t step, const t_commrec *cr,
^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1944:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
andersen_tcoupl(ir, step, cr, md, v, rate,
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
upd->sd->randomize_group, upd->sd->boltzfac);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function 'void update_realloc(gmx_update_t*, int)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'gmx_update_t* init_update(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/wnblist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wnblist.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/disre.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:758:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void constructVsitesGlobal(const gmx_mtop_t &mtop,
^~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/gpubonded-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/gpubonded-impl.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/8/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.3':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-forces.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/listed-internal.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/manage-threading.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/position-restraints.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate-spline-moduli.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald-utils.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long-range-correction.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gather.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-grid.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-load-balancing.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-pp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-redistribute.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-solve.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-only.cpp:72:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spline-work.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-spread.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme-gpu-program-impl.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/logging.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/multisim.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:564:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, &state->s, makeArrayRef(state->s.x), globalXRef);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:869:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
count, nrnb, wcycle, top, &top_global->groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ems->s.lambda, graph, fr, ppForceWorkload, vsite, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_NS : 0),
~~~~~~~~~~~~~~~~~~~~~~~~~
DOMAINDECOMP(cr) ?
~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::yes :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::no,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DOMAINDECOMP(cr) ?
~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::yes :
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::no);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:936:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_md()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:875:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_NS : 0) | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1026:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1051:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
checkpointHandler->isCheckpointingStep(),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bRerunMD, bLastStep,
~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1089:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, upd, constr);
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1292:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_rerun()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:582:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NS | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, const gmx_multisim_t*, gmx::IMDOutputProvider*, t_inputrec*, const MdrunOptions&, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t**, t_nrnb*, real*, t_forcerec*, gmx_enerdata_t**, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**, int, const t_filenm*, gmx_mdoutf**, t_mdebin**, gmx_wallcycle_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:377:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:599:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
isCheckpointingStep, doRerun, isLastStep,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:663:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1932:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<real>(step), &ems.s, state_global, observablesHistory, ems.f);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_mimic()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:465:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, ir, awh, enforcedRotation,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->box, state->x.arrayRefWithPadding(), &state->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->lambda, graph,
~~~~~~~~~~~~~~~~~~~~~
fr, ppForceWorkload, vsite, mu_tot, t, ed,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NS | force_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~
ddOpenBalanceRegion, ddCloseBalanceRegion);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:482:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ir, state, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, fr,
~~~~~~~~~~~~~~~
outf, mdebin, ekind, f,
~~~~~~~~~~~~~~~~~~~~~~~
isCheckpointingStep, doRerun, isLastStep,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mdrunOptions.writeConfout,
~~~~~~~~~~~~~~~~~~~~~~~~~~
bSumEkinhOld);
~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:544:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
dd_collect_vec(cr->dd, state, flocal, ftemp);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:554:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mimicCommunicator.sendForces(ftemp, state_global->natoms);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:569:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
sum_dhdl(enerd, state->lambda, ir->fepvals);
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/8/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, const gmx::PaddedVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::Integrator::do_tpi()':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:647:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
do_force(fplog, cr, ms, inputrec, nullptr, nullptr,
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
step, nrnb, wcycle, top, &top_global->groups,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state_global->lambda,
~~~~~~~~~~~~~~~~~~~~~
nullptr, fr, ppForceWorkload, nullptr, mu_tot, t, nullptr,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) |
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
(bStateChanged ? GMX_FORCE_STATECHANGED : 0),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdOpenBalanceRegionBeforeForceComputation::no,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DdCloseBalanceRegionAfterForceComputation::no);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(gmx::HostVector<T>*, gmx::PinningPolicy) [with T = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/mdmodules.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp: In member function 'int gmx::Mdrunner::mdrunner()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:922:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cr->dd = init_domain_decomposition(mdlog, cr, domdecOptions, mdrunOptions,
~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&mtop, inputrec,
~~~~~~~~~~~~~~~~
box, positionsFromStatePointer(globalState.get()),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&atomSets);
~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1278:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
constructVsitesGlobal(mtop, globalState->x);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::Integrator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:551:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
top_global, step, static_cast<double>(step),
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&state->s, state_global, observablesHistory,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
state->f);
~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicUtils.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/lmfit -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/openmpi-dp/tng/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/baseversion-gen.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:260:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
^~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/MimicCommunicator.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/cmake -P CMakeFiles/libgromacs.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
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cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi-printer.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata-xml.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target compat-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 83%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target listed-forces-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 84%] Built target applied-forces-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
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/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 84%] Built target listed-forces-test
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 85%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 85%] Built target domdec-test
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 88%] Built target commandline-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 88%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 89%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
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Scanning dependencies of target onlinehelp-test
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 89%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 90%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
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cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
Scanning dependencies of target table-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 91%] Built target restraintpotential-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 92%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 93%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/bits/random.h:34,
from /usr/include/c++/8/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 93%] Built target table-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 94%] Built target random-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 94%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 94%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 95%] Built target options-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 95%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[ 97%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[100%] Built target utility-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
cd /<<PKGBUILDDIR>>/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi /<<PKGBUILDDIR>>/build/openmpi/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/openmpi/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi'
(cd build/openmpi ; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/openmpi/lib \
OMPI_MCA_plm_rsh_agent=/bin/false \
OMPI_MCA_rmaps_base_oversubscribe=1 \
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/openmpi/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/openmpi/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/openmpi/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/openmpi/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/openmpi
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (23 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariants
1: [ OK ] ReferenceDataTest.HandlesVariants (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms)
1: [----------] 34 tests from ReferenceDataTest (52 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (8 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (86 ms total)
1: [ PASSED ] 59 tests.
1/27 Test #1: TestUtilsUnitTests ............... Passed 1.27 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "-host" "localhost" "/<<PKGBUILDDIR>>/build/openmpi/bin/testutils-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (0 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (1 ms total)
2: [ PASSED ] 1 test.
2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.68 sec
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3: [==========] Running 50 tests from 8 test cases.
3: [----------] Global test environment set-up.
3: [----------] 1 test from VerletBufferConstraintTest
3: [ RUN ] VerletBufferConstraintTest.EqualMasses
3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
3: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
3:
3: [----------] 3 tests from PrintEbin
3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (8 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (1 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (1 ms)
3: [----------] 3 tests from PrintEbin (10 ms total)
3:
3: [----------] 4 tests from ShakeTest
3: [ RUN ] ShakeTest.ConstrainsOneBond
3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
3: [----------] 4 tests from ShakeTest (0 ms total)
3:
3: [----------] 1 test from NullSignalTest
3: [ RUN ] NullSignalTest.NullSignallerWorks
3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
3: [----------] 1 test from NullSignalTest (0 ms total)
3:
3: [----------] 7 tests from SignalTest
3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
3: [----------] 7 tests from SignalTest (1 ms total)
3:
3: [----------] 9 tests from UpdateGroups
3: [ RUN ] UpdateGroups.ethaneUA
3: [ OK ] UpdateGroups.ethaneUA (0 ms)
3: [ RUN ] UpdateGroups.methane
3: [ OK ] UpdateGroups.methane (0 ms)
3: [ RUN ] UpdateGroups.ethane
3: [ OK ] UpdateGroups.ethane (0 ms)
3: [ RUN ] UpdateGroups.butaneUA
3: [ OK ] UpdateGroups.butaneUA (0 ms)
3: [ RUN ] UpdateGroups.waterThreeSite
3: [ OK ] UpdateGroups.waterThreeSite (0 ms)
3: [ RUN ] UpdateGroups.waterFourSite
3: [ OK ] UpdateGroups.waterFourSite (0 ms)
3: [ RUN ] UpdateGroups.fourAtomsWithSettle
3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
3: [ RUN ] UpdateGroups.waterFlexAngle
3: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
3: [ RUN ] UpdateGroups.twoMoltypes
3: [ OK ] UpdateGroups.twoMoltypes (0 ms)
3: [----------] 9 tests from UpdateGroups (1 ms total)
3:
3: [----------] 1 test from UpdateGroupsCog
3: [ RUN ] UpdateGroupsCog.ComputesCogs
3: [ OK ] UpdateGroupsCog.ComputesCogs (13 ms)
3: [----------] 1 test from UpdateGroupsCog (14 ms total)
3:
3: [----------] 24 tests from WithParameters/SettleTest
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms)
3: [----------] 24 tests from WithParameters/SettleTest (2 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 50 tests from 8 test cases ran. (28 ms total)
3: [ PASSED ] 50 tests.
3/27 Test #3: MdlibUnitTest .................... Passed 0.61 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4: [==========] Running 3 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 3 tests from ElectricFieldTest
4: [ RUN ] ElectricFieldTest.Static
4: [ OK ] ElectricFieldTest.Static (0 ms)
4: [ RUN ] ElectricFieldTest.Oscillating
4: [ OK ] ElectricFieldTest.Oscillating (1 ms)
4: [ RUN ] ElectricFieldTest.Pulsed
4: [ OK ] ElectricFieldTest.Pulsed (0 ms)
4: [----------] 3 tests from ElectricFieldTest (1 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 3 tests from 1 test case ran. (1 ms total)
4: [ PASSED ] 3 tests.
4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.49 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 15 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 15 tests from BondedTest
5: [ RUN ] BondedTest.BondAnglePbcNone
5: [ OK ] BondedTest.BondAnglePbcNone (1 ms)
5: [ RUN ] BondedTest.BondAnglePbcXy
5: [ OK ] BondedTest.BondAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.BondAnglePbcXyz
5: [ OK ] BondedTest.BondAnglePbcXyz (1 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcNone
5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXy
5: [ OK ] BondedTest.DihedralAnglePbcXy (1 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXyz
5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcNo
5: [ OK ] BondedTest.IfuncBondsPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXy
5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXyz
5: [ OK ] BondedTest.IfuncBondsPbcXyz (1 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcNo
5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXy
5: [ OK ] BondedTest.IfuncAnglesPbcXy (1 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ
5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (5 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo
5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (1 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms)
5: [----------] 15 tests from BondedTest (12 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 15 tests from 1 test case ran. (13 ms total)
5: [ PASSED ] 15 tests.
5/27 Test #5: ListedForcesTest ................. Passed 0.52 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6: [==========] Running 55 tests from 6 test cases.
6: [----------] Global test environment set-up.
6: [----------] 3 tests from CommandLineHelpModuleTest
6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms)
6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (53 ms)
6: [----------] 3 tests from CommandLineHelpModuleTest (56 ms total)
6:
6: [----------] 6 tests from CommandLineHelpWriterTest
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
6: [----------] 6 tests from CommandLineHelpWriterTest (6 ms total)
6:
6: [----------] 6 tests from CommandLineModuleManagerTest
6: [ RUN ] CommandLineModuleManagerTest.RunsModule
6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total)
6:
6: [----------] 13 tests from CommandLineParserTest
6: [ RUN ] CommandLineParserTest.HandlesSingleValues
6: [ OK ] CommandLineParserTest.HandlesSingleValues (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesString
6: [ OK ] CommandLineParserTest.HandlesString (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
6: [----------] 13 tests from CommandLineParserTest (2 ms total)
6:
6: [----------] 6 tests from CommandLineProgramContextTest
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (1 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
6:
6: [----------] 21 tests from ParseCommonArgsTest
6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (1 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (3 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (2 ms)
6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
6: [----------] 21 tests from ParseCommonArgsTest (12 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 55 tests from 6 test cases ran. (79 ms total)
6: [ PASSED ] 55 tests.
6/27 Test #6: CommandLineUnitTests ............. Passed 0.54 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 9 tests from 2 test cases.
7: [----------] Global test environment set-up.
7: [----------] 7 tests from HashedMap
7: [ RUN ] HashedMap.InsertsFinds
7: [ OK ] HashedMap.InsertsFinds (0 ms)
7: [ RUN ] HashedMap.NegativeKeysWork
7: [ OK ] HashedMap.NegativeKeysWork (0 ms)
7: [ RUN ] HashedMap.InsertsErases
7: [ OK ] HashedMap.InsertsErases (0 ms)
7: [ RUN ] HashedMap.InsertsOrAssigns
7: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
7: [ RUN ] HashedMap.Clears
7: [ OK ] HashedMap.Clears (0 ms)
7: [ RUN ] HashedMap.LinkedEntries
7: [ OK ] HashedMap.LinkedEntries (0 ms)
7: [ RUN ] HashedMap.ResizesTable
7: [ OK ] HashedMap.ResizesTable (0 ms)
7: [----------] 7 tests from HashedMap (1 ms total)
7:
7: [----------] 2 tests from LocalAtomSetManager
7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
7: [----------] 2 tests from LocalAtomSetManager (0 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 9 tests from 2 test cases ran. (1 ms total)
7: [ PASSED ] 9 tests.
7/27 Test #7: DomDecTests ...................... Passed 0.42 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 257 tests from 10 test cases.
8: [----------] Global test environment set-up.
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (12 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (12 ms total)
8:
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (62 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (16 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (16 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (20 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (11 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (11 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (11 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (27 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (12 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (13 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (15 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (16 ms)
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (391 ms total)
8:
8: [----------] 144 tests from SaneInput/PmeGatherTest
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (7 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
8: [----------] 144 tests from SaneInput/PmeGatherTest (213 ms total)
8:
8: [----------] 16 tests from SaneInput/PmeSolveTest
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (6 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (7 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (4 ms)
8: [----------] 16 tests from SaneInput/PmeSolveTest (67 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (22 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (6 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (37 ms total)
8:
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (6 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (5 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (4 ms)
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (64 ms total)
8:
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (9 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (20 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (11 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (11 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (7 ms)
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (104 ms total)
8:
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (10 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (12 ms)
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (88 ms total)
8:
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (15 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (15 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (22 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (25 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (31 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (35 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (15 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (16 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (17 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (20 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (24 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (27 ms)
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (278 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 257 tests from 10 test cases ran. (1307 ms total)
8: [ PASSED ] 257 tests.
8/27 Test #8: EwaldUnitTests ................... Passed 1.89 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 14 tests from 4 test cases.
9: [----------] Global test environment set-up.
9: [----------] 2 tests from ManyFFTTest
9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (77 ms)
9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (42 ms)
9: [----------] 2 tests from ManyFFTTest (123 ms total)
9:
9: [----------] 1 test from FFTTest
9: [ RUN ] FFTTest.Real2DLength18_15Test
9: [ OK ] FFTTest.Real2DLength18_15Test (19 ms)
9: [----------] 1 test from FFTTest (21 ms total)
9:
9: [----------] 1 test from FFFTest3D
9: [ RUN ] FFFTest3D.Real5_6_9
9: [ OK ] FFFTest3D.Real5_6_9 (10 ms)
9: [----------] 1 test from FFFTest3D (11 ms total)
9:
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (12 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (27 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (9 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (3 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (33 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (43 ms)
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (138 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 14 tests from 4 test cases ran. (295 ms total)
9: [ PASSED ] 14 tests.
9/27 Test #9: FFTUnitTests ..................... Passed 0.81 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 60 tests from 19 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/0 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/1 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/2 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Swap
10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Comparison
10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Swap
10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Comparison
10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Swap
10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Comparison
10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Swap
10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Comparison
10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/3 (2 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (1 ms total)
10:
10: [----------] 1 test from HostAllocatorUntypedTest
10: [ RUN ] HostAllocatorUntypedTest.Comparison
10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
10:
10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/0 (2 ms total)
10:
10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/1 (2 ms total)
10:
10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/2 (2 ms total)
10:
10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 60 tests from 19 test cases ran. (21 ms total)
10: [ PASSED ] 60 tests.
10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.48 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 4 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 4 tests from HardwareTopologyTest
11: [ RUN ] HardwareTopologyTest.Execute
11: [ OK ] HardwareTopologyTest.Execute (27 ms)
11: [ RUN ] HardwareTopologyTest.HwlocExecute
11: [ OK ] HardwareTopologyTest.HwlocExecute (25 ms)
11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (28 ms)
11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (36 ms)
11: [----------] 4 tests from HardwareTopologyTest (116 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 4 tests from 1 test case ran. (116 ms total)
11: [ PASSED ] 4 tests.
11/27 Test #11: HardwareUnitTests ................ Passed 0.60 sec
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 112 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from EmptyArrayRefWithPaddingTest
12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyArrayRefWithPaddingTest (1 ms total)
12:
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
12:
12: [----------] 6 tests from StructureSimilarityTest
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
12: [----------] 6 tests from StructureSimilarityTest (0 ms total)
12:
12: [----------] 21 tests from FunctionTest
12: [ RUN ] FunctionTest.StaticLog2
12: [ OK ] FunctionTest.StaticLog2 (10 ms)
12: [ RUN ] FunctionTest.Log2I32Bit
12: [ OK ] FunctionTest.Log2I32Bit (0 ms)
12: [ RUN ] FunctionTest.Log2I64Bit
12: [ OK ] FunctionTest.Log2I64Bit (1 ms)
12: [ RUN ] FunctionTest.GreatestCommonDivisor
12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
12: [ RUN ] FunctionTest.InvsqrtFloat
12: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
12: [ RUN ] FunctionTest.InvsqrtDouble
12: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
12: [ RUN ] FunctionTest.InvsqrtInteger
12: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
12: [ RUN ] FunctionTest.InvcbrtFloat
12: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
12: [ RUN ] FunctionTest.InvcbrtDouble
12: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
12: [ RUN ] FunctionTest.InvcbrtInteger
12: [ OK ] FunctionTest.InvcbrtInteger (1 ms)
12: [ RUN ] FunctionTest.SixthrootFloat
12: [ OK ] FunctionTest.SixthrootFloat (0 ms)
12: [ RUN ] FunctionTest.SixthrootDouble
12: [ OK ] FunctionTest.SixthrootDouble (1 ms)
12: [ RUN ] FunctionTest.SixthrootInteger
12: [ OK ] FunctionTest.SixthrootInteger (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootFloat
12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootDouble
12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootInteger
12: [ OK ] FunctionTest.InvsixthrootInteger (68 ms)
12: [ RUN ] FunctionTest.Powers
12: [ OK ] FunctionTest.Powers (0 ms)
12: [ RUN ] FunctionTest.ErfInvFloat
12: [ OK ] FunctionTest.ErfInvFloat (0 ms)
12: [ RUN ] FunctionTest.ErfInvDouble
12: [ OK ] FunctionTest.ErfInvDouble (1 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
12: [----------] 21 tests from FunctionTest (86 ms total)
12:
12: [----------] 2 tests from InvertMatrixTest
12: [ RUN ] InvertMatrixTest.IdentityIsImpotent
12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertMatrixTest.ComputesInverse
12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
12: [----------] 2 tests from InvertMatrixTest (1 ms total)
12:
12: [----------] 2 tests from InvertBoxMatrixTest
12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanCopyAssign
12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanMoveAssign
12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanSwap
12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanCopyAssign
12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanMoveAssign
12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanSwap
12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (1 ms)
12: [ RUN ] PaddedVectorTest/2.CanCopyAssign
12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanMoveAssign
12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanSwap
12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/2 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanCopyAssign
12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanMoveAssign
12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanSwap
12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanCopyAssign
12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanMoveAssign
12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanSwap
12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanCopyAssign
12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanMoveAssign
12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanSwap
12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/5 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanCopyAssign
12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanMoveAssign
12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanSwap
12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanCopyAssign
12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanMoveAssign
12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanSwap
12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanCopyAssign
12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanMoveAssign
12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanSwap
12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (1 ms)
12: [ RUN ] PaddedVectorTest/9.CanCopyAssign
12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanMoveAssign
12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanSwap
12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total)
12:
12: [----------] 33 tests from RVecTest
12: [ RUN ] RVecTest.CanBeStoredInVector
12: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAsMutable_rvec
12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Array
12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
12: [ RUN ] RVecTest.CanAddRVecToRvec
12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanAddAssignRVecToRvec
12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractRVecFromRvec
12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanDotProductRVecByRvec
12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanCrossProductRVecByRvec
12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVecInplace
12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
12: [ RUN ] RVecTest.CanScaleRVec
12: [ OK ] RVecTest.CanScaleRVec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVec
12: [ OK ] RVecTest.CanDivideRVec (0 ms)
12: [ RUN ] RVecTest.CanDoUnitvFromRVec
12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanSqLengthOfRVec
12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanLengthOfRVec
12: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToRVec
12: [ OK ] RVecTest.CanCastToRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToDVec
12: [ OK ] RVecTest.CanCastToDVec (0 ms)
12: [ RUN ] RVecTest.CanLeftScalarMultiply
12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanRightScalarMultiply
12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanGetUnitvFromRVec
12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanGetSqLengthOfRVec
12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanGetLengthOfRVec
12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoCrossProductOfRVec
12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoDotProductOfRVec
12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
12: [ RUN ] RVecTest.WorksAs_dvec_Reference
12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_ivec_Reference
12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Reference
12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
12: [ RUN ] RVecTest.CopyConstructorWorks
12: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
12: [ RUN ] RVecTest.CopyAssignmentWorks
12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
12: [ RUN ] RVecTest.MoveConstructorWorks
12: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
12: [ RUN ] RVecTest.MoveAssignmentWorks
12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
12: [----------] 33 tests from RVecTest (1 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 112 tests from 20 test cases ran. (93 ms total)
12: [ PASSED ] 112 tests.
12/27 Test #12: MathUnitTests .................... Passed 0.57 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 17 tests from ThreadAffinityTest
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
13: NOTE: Affinity setting failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
13: NOTE: Affinity setting for 1/2 threads failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms)
13: [----------] 17 tests from ThreadAffinityTest (13 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 1 test case ran. (13 ms total)
13: [ PASSED ] 17 tests.
13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.48 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/openmpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 13 tests from 2 test cases.
14: [----------] Global test environment set-up.
14: [----------] 6 tests from ThreadAffinityMultiRankTest
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (5 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (3 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (2 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (1 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (2 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (2 ms)
14: [----------] 6 tests from ThreadAffinityMultiRankTest (16 ms total)
14:
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (3 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (2 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (2 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (2 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (2 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (3 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (2 ms)
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (20 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 13 tests from 2 test cases ran. (36 ms total)
14: [ PASSED ] 13 tests.
14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.77 sec
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 22 tests from 4 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from TextTableFormatterTest
15: [ RUN ] TextTableFormatterTest.HandlesBasicCase
15: [ OK ] TextTableFormatterTest.HandlesBasicCase (17 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesIndentation
15: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
15: [----------] 6 tests from TextTableFormatterTest (19 ms total)
15:
15: [----------] 3 tests from HelpManagerTest
15: [ RUN ] HelpManagerTest.HandlesRootTopic
15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
15: [ RUN ] HelpManagerTest.HandlesSubTopics
15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
15: [ RUN ] HelpManagerTest.HandlesInvalidTopics
15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
15: [----------] 3 tests from HelpManagerTest (2 ms total)
15:
15: [----------] 2 tests from HelpTopicFormattingTest
15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
15:
15: [----------] 11 tests from HelpWriterContextTest
15: [ RUN ] HelpWriterContextTest.FormatsParagraphs
15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralText
15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsBulletList
15: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsGridTable
15: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsTitles
15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
15: [----------] 11 tests from HelpWriterContextTest (6 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 22 tests from 4 test cases ran. (30 ms total)
15: [ PASSED ] 22 tests.
15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.54 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 110 tests from 18 test cases.
16: [----------] Global test environment set-up.
16: [----------] 5 tests from AbstractOptionStorageTest
16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms)
16: [----------] 5 tests from AbstractOptionStorageTest (2 ms total)
16:
16: [----------] 8 tests from FileNameOptionTest
16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (1 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
16: [----------] 8 tests from FileNameOptionTest (1 ms total)
16:
16: [----------] 15 tests from FileNameOptionManagerTest
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (1 ms)
16: [----------] 15 tests from FileNameOptionManagerTest (2 ms total)
16:
16: [----------] 1 test from OptionsTest
16: [ RUN ] OptionsTest.FailsOnNonsafeStorage
16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
16: [----------] 1 test from OptionsTest (0 ms total)
16:
16: [----------] 9 tests from OptionsAssignerTest
16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMissingValue
16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesExtraValue
16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesGroups
16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesSections
16: [ OK ] OptionsAssignerTest.HandlesSections (1 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
16: [----------] 9 tests from OptionsAssignerTest (1 ms total)
16:
16: [----------] 4 tests from OptionsAssignerBooleanTest
16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total)
16:
16: [----------] 13 tests from OptionsAssignerIntegerTest
16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
16: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total)
16:
16: [----------] 5 tests from OptionsAssignerDoubleTest
16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
16:
16: [----------] 9 tests from OptionsAssignerStringTest
16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
16:
16: [----------] 6 tests from OptionsAssignerEnumTest
16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
16:
16: [----------] 8 tests from RepeatingOptionSectionTest
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total)
16:
16: [----------] 1 test from TimeUnitManagerTest
16: [ RUN ] TimeUnitManagerTest.BasicOperations
16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
16: [----------] 1 test from TimeUnitManagerTest (0 ms total)
16:
16: [----------] 4 tests from TimeUnitBehaviorTest
16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total)
16:
16: [----------] 2 tests from TreeValueSupportAssignTest
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
16:
16: [----------] 1 test from TreeValueSupportAssignErrorTest
16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
16:
16: [----------] 5 tests from TreeValueSupportCheckTest
16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
16:
16: [----------] 6 tests from TreeValueSupportAdjustTest
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
16: [----------] 6 tests from TreeValueSupportAdjustTest (3 ms total)
16:
16: [----------] 8 tests from TreeValueSupportTest
16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsInt64Option
16: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsStringOption
16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsFloatOption
16: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumOption
16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms)
16: [----------] 8 tests from TreeValueSupportTest (4 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 110 tests from 18 test cases ran. (17 ms total)
16: [ PASSED ] 110 tests.
16/27 Test #16: OptionsUnitTests ................. Passed 0.52 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 44 tests from 10 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from ExponentialDistributionTest
17: [ RUN ] ExponentialDistributionTest.Output
17: [ OK ] ExponentialDistributionTest.Output (2 ms)
17: [ RUN ] ExponentialDistributionTest.Logical
17: [ OK ] ExponentialDistributionTest.Logical (0 ms)
17: [ RUN ] ExponentialDistributionTest.Reset
17: [ OK ] ExponentialDistributionTest.Reset (0 ms)
17: [ RUN ] ExponentialDistributionTest.AltParam
17: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from ExponentialDistributionTest (3 ms total)
17:
17: [----------] 4 tests from GammaDistributionTest
17: [ RUN ] GammaDistributionTest.Output
17: [ OK ] GammaDistributionTest.Output (1 ms)
17: [ RUN ] GammaDistributionTest.Logical
17: [ OK ] GammaDistributionTest.Logical (0 ms)
17: [ RUN ] GammaDistributionTest.Reset
17: [ OK ] GammaDistributionTest.Reset (0 ms)
17: [ RUN ] GammaDistributionTest.AltParam
17: [ OK ] GammaDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from GammaDistributionTest (2 ms total)
17:
17: [----------] 4 tests from NormalDistributionTest
17: [ RUN ] NormalDistributionTest.Output
17: [ OK ] NormalDistributionTest.Output (1 ms)
17: [ RUN ] NormalDistributionTest.Logical
17: [ OK ] NormalDistributionTest.Logical (0 ms)
17: [ RUN ] NormalDistributionTest.Reset
17: [ OK ] NormalDistributionTest.Reset (0 ms)
17: [ RUN ] NormalDistributionTest.AltParam
17: [ OK ] NormalDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from NormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from SeedTest
17: [ RUN ] SeedTest.makeRandomSeed
17: [ OK ] SeedTest.makeRandomSeed (1 ms)
17: [----------] 1 test from SeedTest (1 ms total)
17:
17: [----------] 6 tests from TabulatedNormalDistributionTest
17: [ RUN ] TabulatedNormalDistributionTest.Output14
17: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Output16
17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Logical
17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Reset
17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.AltParam
17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
17: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
17:
17: [----------] 1 test from TabulatedNormalDistributionTableTest
17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (6 ms)
17: [----------] 1 test from TabulatedNormalDistributionTableTest (6 ms total)
17:
17: [----------] 6 tests from ThreeFry2x64Test
17: [ RUN ] ThreeFry2x64Test.Logical
17: [ OK ] ThreeFry2x64Test.Logical (0 ms)
17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
17: [ RUN ] ThreeFry2x64Test.Reseed
17: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
17: [ RUN ] ThreeFry2x64Test.Discard
17: [ OK ] ThreeFry2x64Test.Discard (0 ms)
17: [ RUN ] ThreeFry2x64Test.InvalidCounter
17: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms)
17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
17: [----------] 6 tests from ThreeFry2x64Test (2 ms total)
17:
17: [----------] 4 tests from UniformIntDistributionTest
17: [ RUN ] UniformIntDistributionTest.Output
17: [ OK ] UniformIntDistributionTest.Output (1 ms)
17: [ RUN ] UniformIntDistributionTest.Logical
17: [ OK ] UniformIntDistributionTest.Logical (0 ms)
17: [ RUN ] UniformIntDistributionTest.Reset
17: [ OK ] UniformIntDistributionTest.Reset (0 ms)
17: [ RUN ] UniformIntDistributionTest.AltParam
17: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
17:
17: [----------] 5 tests from UniformRealDistributionTest
17: [ RUN ] UniformRealDistributionTest.GenerateCanonical
17: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
17: [ RUN ] UniformRealDistributionTest.Output
17: [ OK ] UniformRealDistributionTest.Output (1 ms)
17: [ RUN ] UniformRealDistributionTest.Logical
17: [ OK ] UniformRealDistributionTest.Logical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Reset
17: [ OK ] UniformRealDistributionTest.Reset (0 ms)
17: [ RUN ] UniformRealDistributionTest.AltParam
17: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
17: [----------] 5 tests from UniformRealDistributionTest (2 ms total)
17:
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (4 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 44 tests from 10 test cases ran. (26 ms total)
17: [ PASSED ] 44 tests.
17/27 Test #17: RandomUnitTests .................. Passed 0.54 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 1 test from 1 test case.
18: [----------] Global test environment set-up.
18: [----------] 1 test from RestraintManager
18: [ RUN ] RestraintManager.restraintList
18: [ OK ] RestraintManager.restraintList (0 ms)
18: [----------] 1 test from RestraintManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 1 test from 1 test case ran. (2 ms total)
18: [ PASSED ] 1 test.
18/27 Test #18: RestraintTests ................... Passed 0.45 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 16 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
19: [ RUN ] SplineTableTest/0.Sinc
19: [ OK ] SplineTableTest/0.Sinc (3 ms)
19: [ RUN ] SplineTableTest/0.LJ12
19: [ OK ] SplineTableTest/0.LJ12 (86 ms)
19: [ RUN ] SplineTableTest/0.PmeCorrection
19: [ OK ] SplineTableTest/0.PmeCorrection (5 ms)
19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (4 ms)
19: [ RUN ] SplineTableTest/0.TwoFunctions
19: [ OK ] SplineTableTest/0.TwoFunctions (172 ms)
19: [ RUN ] SplineTableTest/0.ThreeFunctions
19: [ OK ] SplineTableTest/0.ThreeFunctions (188 ms)
19: [----------] 8 tests from SplineTableTest/0 (467 ms total)
19:
19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
19: [ RUN ] SplineTableTest/1.Sinc
19: [ OK ] SplineTableTest/1.Sinc (2 ms)
19: [ RUN ] SplineTableTest/1.LJ12
19: [ OK ] SplineTableTest/1.LJ12 (15 ms)
19: [ RUN ] SplineTableTest/1.PmeCorrection
19: [ OK ] SplineTableTest/1.PmeCorrection (6 ms)
19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (5 ms)
19: [ RUN ] SplineTableTest/1.TwoFunctions
19: [ OK ] SplineTableTest/1.TwoFunctions (31 ms)
19: [ RUN ] SplineTableTest/1.ThreeFunctions
19: [ OK ] SplineTableTest/1.ThreeFunctions (33 ms)
19: [----------] 8 tests from SplineTableTest/1 (102 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 16 tests from 2 test cases ran. (569 ms total)
19: [ PASSED ] 16 tests.
19/27 Test #19: TableUnitTests ................... Passed 1.05 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 1 test case.
20: [----------] Global test environment set-up.
20: [----------] 3 tests from GpuIdStringHandlingTest
20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork
20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid
20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow
20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms)
20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 1 test case ran. (1 ms total)
20: [ PASSED ] 3 tests.
20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.46 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 325 tests from 52 test cases.
21: [----------] Global test environment set-up.
21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.Move
21: [ OK ] AllocatorTest/0.Move (0 ms)
21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/0 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.Move
21: [ OK ] AllocatorTest/1.Move (0 ms)
21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/1 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.Move
21: [ OK ] AllocatorTest/2.Move (0 ms)
21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/2 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.Move
21: [ OK ] AllocatorTest/3.Move (0 ms)
21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/3 (0 ms total)
21:
21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.Move
21: [ OK ] AllocatorTest/4.Move (0 ms)
21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/4 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.Move
21: [ OK ] AllocatorTest/5.Move (0 ms)
21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/5 (1 ms total)
21:
21: [----------] 1 test from AllocatorUntypedTest
21: [ RUN ] AllocatorUntypedTest.Comparison
21: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
21: [----------] 1 test from AllocatorUntypedTest (0 ms total)
21:
21: [----------] 1 test from EmptyArrayRefTest
21: [ RUN ] EmptyArrayRefTest.IsEmpty
21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyArrayRefTest (0 ms total)
21:
21: [----------] 1 test from EmptyConstArrayRefTest
21: [ RUN ] EmptyConstArrayRefTest.IsEmpty
21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (1 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/5 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/6 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (1 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/7 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (1 ms)
21: [----------] 9 tests from ArrayRefTest/9 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/14 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
21:
21: [----------] 4 tests from KeyValueTreeSerializerTest
21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms)
21: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total)
21:
21: [----------] 6 tests from TreeValueTransformTest
21: [ RUN ] TreeValueTransformTest.SimpleTransforms
21: [ OK ] TreeValueTransformTest.SimpleTransforms (1 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromString
21: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
21: [ RUN ] TreeValueTransformTest.ScopedTransformRules
21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
21: [----------] 6 tests from TreeValueTransformTest (3 ms total)
21:
21: [----------] 1 test from TreeValueTransformErrorTest
21: [ RUN ] TreeValueTransformErrorTest.ConversionError
21: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
21: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
21:
21: [----------] 2 tests from RegexBasicTest
21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported
21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms)
21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported
21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms)
21: [----------] 2 tests from RegexBasicTest (2 ms total)
21:
21: [----------] 5 tests from LoggerTest
21: [ RUN ] LoggerTest.EmptyLoggerWorks
21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
21: [ RUN ] LoggerTest.LogsToStream
21: [ OK ] LoggerTest.LogsToStream (1 ms)
21: [ RUN ] LoggerTest.LogsToFile
21: [ OK ] LoggerTest.LogsToFile (1 ms)
21: [ RUN ] LoggerTest.LevelFilteringWorks
21: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
21: [ RUN ] LoggerTest.LogsToMultipleStreams
21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
21: [----------] 5 tests from LoggerTest (3 ms total)
21:
21: [----------] 4 tests from MutexBasicTest
21: [ RUN ] MutexBasicTest.CanBeMade
21: [ OK ] MutexBasicTest.CanBeMade (0 ms)
21: [ RUN ] MutexBasicTest.CanBeLocked
21: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeTryLocked
21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
21: [----------] 4 tests from MutexBasicTest (0 ms total)
21:
21: [----------] 3 tests from MutexTaskTest
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
21: [----------] 3 tests from MutexTaskTest (1 ms total)
21:
21: [----------] 4 tests from PathTest
21: [ RUN ] PathTest.StripSourcePrefixWorks
21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks
21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathWorks
21: [ OK ] PathTest.GetParentPathWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathAndBasenameWorks
21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms)
21: [----------] 4 tests from PathTest (1 ms total)
21:
21: [----------] 2 tests from PhysicalNodeCommunicatorTest
21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
21:
21: [----------] 7 tests from StringUtilityTest
21: [ RUN ] StringUtilityTest.StartsWith
21: [ OK ] StringUtilityTest.StartsWith (0 ms)
21: [ RUN ] StringUtilityTest.EndsWith
21: [ OK ] StringUtilityTest.EndsWith (0 ms)
21: [ RUN ] StringUtilityTest.StripSuffixIfPresent
21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
21: [ RUN ] StringUtilityTest.StripString
21: [ OK ] StringUtilityTest.StripString (0 ms)
21: [ RUN ] StringUtilityTest.SplitString
21: [ OK ] StringUtilityTest.SplitString (0 ms)
21: [ RUN ] StringUtilityTest.SplitDelimitedString
21: [ OK ] StringUtilityTest.SplitDelimitedString (1 ms)
21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms)
21: [----------] 7 tests from StringUtilityTest (1 ms total)
21:
21: [----------] 2 tests from FormatStringTest
21: [ RUN ] FormatStringTest.HandlesBasicFormatting
21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
21: [ RUN ] FormatStringTest.HandlesLongStrings
21: [ OK ] FormatStringTest.HandlesLongStrings (1 ms)
21: [----------] 2 tests from FormatStringTest (1 ms total)
21:
21: [----------] 1 test from StringFormatterTest
21: [ RUN ] StringFormatterTest.HandlesBasicFormatting
21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
21: [----------] 1 test from StringFormatterTest (0 ms total)
21:
21: [----------] 1 test from formatAndJoinTest
21: [ RUN ] formatAndJoinTest.Works
21: [ OK ] formatAndJoinTest.Works (0 ms)
21: [----------] 1 test from formatAndJoinTest (0 ms total)
21:
21: [----------] 1 test from JoinStringsTest
21: [ RUN ] JoinStringsTest.Works
21: [ OK ] JoinStringsTest.Works (0 ms)
21: [----------] 1 test from JoinStringsTest (0 ms total)
21:
21: [----------] 6 tests from ReplaceAllTest
21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesNoMatches
21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
21: [----------] 6 tests from ReplaceAllTest (0 ms total)
21:
21: [----------] 10 tests from TextLineWrapperTest
21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (1 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectly
21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndent
21: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
21: [----------] 10 tests from TextLineWrapperTest (3 ms total)
21:
21: [----------] 6 tests from TextWriterTest
21: [ RUN ] TextWriterTest.WritesLines
21: [ OK ] TextWriterTest.WritesLines (0 ms)
21: [ RUN ] TextWriterTest.WritesLinesInParts
21: [ OK ] TextWriterTest.WritesLinesInParts (1 ms)
21: [ RUN ] TextWriterTest.WritesWrappedLines
21: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
21: [ RUN ] TextWriterTest.TracksNewlines
21: [ OK ] TextWriterTest.TracksNewlines (1 ms)
21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
21: [----------] 6 tests from TextWriterTest (2 ms total)
21:
21: [----------] 1 test from TypeTraitsTest
21: [ RUN ] TypeTraitsTest.IsIntegralConstant
21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
21: [----------] 1 test from TypeTraitsTest (0 ms total)
21:
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
21:
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
21:
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
21:
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (2 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (3 ms total)
21:
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 325 tests from 52 test cases ran. (41 ms total)
21: [ PASSED ] 325 tests.
21/27 Test #21: UtilityUnitTests ................. Passed 0.59 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/openmpi/bin/utility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 2 tests from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from PhysicalNodeCommunicatorTest
22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
22: [----------] 2 tests from PhysicalNodeCommunicatorTest (4 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 2 tests from 1 test case ran. (4 ms total)
22: [ PASSED ] 2 tests.
22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.76 sec
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 17 tests from 4 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from FileMD5Test
23: [ RUN ] FileMD5Test.CanComputeMD5
23: [ OK ] FileMD5Test.CanComputeMD5 (5 ms)
23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
23: [----------] 2 tests from FileMD5Test (6 ms total)
23:
23: [----------] 9 tests from ReadTest
23: [ RUN ] ReadTest.get_eint_ReadsInteger
23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_eint64_ReadsInteger
23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (1 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsInteger
23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsFloat
23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
23: [ RUN ] ReadTest.get_ereal_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not a
23: real value
23:
23:
23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
23: [----------] 9 tests from ReadTest (3 ms total)
23:
23: [----------] 2 tests from TngTest
23: [ RUN ] TngTest.CanOpenTngFile
23: [ OK ] TngTest.CanOpenTngFile (0 ms)
23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
23: [----------] 2 tests from TngTest (1 ms total)
23:
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (74 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (86 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 17 tests from 4 test cases ran. (100 ms total)
23: [ PASSED ] 17 tests.
23/27 Test #23: FileIOTests ...................... Passed 0.57 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 5 tests from 1 test case.
24: [----------] Global test environment set-up.
24: [----------] 5 tests from PullTest
24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
24: [----------] 5 tests from PullTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 5 tests from 1 test case ran. (2 ms total)
24: [ PASSED ] 5 tests.
24/27 Test #24: PullTest ......................... Passed 0.46 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 12 tests from 4 test cases.
25: [----------] Global test environment set-up.
25: [----------] 1 test from BiasTest
25: [ RUN ] BiasTest.DetectsCovering
25: [ OK ] BiasTest.DetectsCovering (4 ms)
25: [----------] 1 test from BiasTest (4 ms total)
25:
25: [----------] 1 test from gridTest
25: [ RUN ] gridTest.neighborhood
25: [ OK ] gridTest.neighborhood (7 ms)
25: [----------] 1 test from gridTest (7 ms total)
25:
25: [----------] 8 tests from WithParameters/BiasTest
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (52 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (3 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (5 ms)
25: [----------] 8 tests from WithParameters/BiasTest (78 ms total)
25:
25: [----------] 2 tests from WithParameters/BiasStateTest
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
25: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 12 tests from 4 test cases ran. (95 ms total)
25: [ PASSED ] 12 tests.
25/27 Test #25: AwhTest .......................... Passed 0.64 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 86 tests from 3 test cases.
26: [----------] Global test environment set-up.
26: [----------] 41 tests from SimdScalarTest
26: [ RUN ] SimdScalarTest.load
26: [ OK ] SimdScalarTest.load (0 ms)
26: [ RUN ] SimdScalarTest.loadU
26: [ OK ] SimdScalarTest.loadU (0 ms)
26: [ RUN ] SimdScalarTest.store
26: [ OK ] SimdScalarTest.store (0 ms)
26: [ RUN ] SimdScalarTest.storeU
26: [ OK ] SimdScalarTest.storeU (0 ms)
26: [ RUN ] SimdScalarTest.setZero
26: [ OK ] SimdScalarTest.setZero (0 ms)
26: [ RUN ] SimdScalarTest.andNot
26: [ OK ] SimdScalarTest.andNot (0 ms)
26: [ RUN ] SimdScalarTest.fma
26: [ OK ] SimdScalarTest.fma (0 ms)
26: [ RUN ] SimdScalarTest.fms
26: [ OK ] SimdScalarTest.fms (0 ms)
26: [ RUN ] SimdScalarTest.fnma
26: [ OK ] SimdScalarTest.fnma (0 ms)
26: [ RUN ] SimdScalarTest.fnms
26: [ OK ] SimdScalarTest.fnms (0 ms)
26: [ RUN ] SimdScalarTest.maskAdd
26: [ OK ] SimdScalarTest.maskAdd (0 ms)
26: [ RUN ] SimdScalarTest.maskzMul
26: [ OK ] SimdScalarTest.maskzMul (0 ms)
26: [ RUN ] SimdScalarTest.maskzFma
26: [ OK ] SimdScalarTest.maskzFma (0 ms)
26: [ RUN ] SimdScalarTest.abs
26: [ OK ] SimdScalarTest.abs (0 ms)
26: [ RUN ] SimdScalarTest.max
26: [ OK ] SimdScalarTest.max (0 ms)
26: [ RUN ] SimdScalarTest.min
26: [ OK ] SimdScalarTest.min (0 ms)
26: [ RUN ] SimdScalarTest.round
26: [ OK ] SimdScalarTest.round (0 ms)
26: [ RUN ] SimdScalarTest.trunc
26: [ OK ] SimdScalarTest.trunc (0 ms)
26: [ RUN ] SimdScalarTest.reduce
26: [ OK ] SimdScalarTest.reduce (0 ms)
26: [ RUN ] SimdScalarTest.testBits
26: [ OK ] SimdScalarTest.testBits (0 ms)
26: [ RUN ] SimdScalarTest.anyTrue
26: [ OK ] SimdScalarTest.anyTrue (0 ms)
26: [ RUN ] SimdScalarTest.selectByMask
26: [ OK ] SimdScalarTest.selectByMask (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMask
26: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
26: [ RUN ] SimdScalarTest.blend
26: [ OK ] SimdScalarTest.blend (0 ms)
26: [ RUN ] SimdScalarTest.cvtR2I
26: [ OK ] SimdScalarTest.cvtR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvttR2I
26: [ OK ] SimdScalarTest.cvttR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvtI2R
26: [ OK ] SimdScalarTest.cvtI2R (0 ms)
26: [ RUN ] SimdScalarTest.cvtF2D
26: [ OK ] SimdScalarTest.cvtF2D (0 ms)
26: [ RUN ] SimdScalarTest.cvtD2D
26: [ OK ] SimdScalarTest.cvtD2D (0 ms)
26: [ RUN ] SimdScalarTest.loadI
26: [ OK ] SimdScalarTest.loadI (0 ms)
26: [ RUN ] SimdScalarTest.loadUI
26: [ OK ] SimdScalarTest.loadUI (0 ms)
26: [ RUN ] SimdScalarTest.storeI
26: [ OK ] SimdScalarTest.storeI (0 ms)
26: [ RUN ] SimdScalarTest.storeUI
26: [ OK ] SimdScalarTest.storeUI (0 ms)
26: [ RUN ] SimdScalarTest.andNotI
26: [ OK ] SimdScalarTest.andNotI (0 ms)
26: [ RUN ] SimdScalarTest.testBitsI
26: [ OK ] SimdScalarTest.testBitsI (0 ms)
26: [ RUN ] SimdScalarTest.selectByMaskI
26: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMaskI
26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
26: [ RUN ] SimdScalarTest.blendI
26: [ OK ] SimdScalarTest.blendI (0 ms)
26: [ RUN ] SimdScalarTest.cvtB2IB
26: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
26: [ RUN ] SimdScalarTest.cvtIB2B
26: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
26: [ RUN ] SimdScalarTest.expandScalarsToTriplets
26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
26: [----------] 41 tests from SimdScalarTest (10 ms total)
26:
26: [----------] 8 tests from SimdScalarUtilTest
26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
26: [----------] 8 tests from SimdScalarUtilTest (2 ms total)
26:
26: [----------] 37 tests from SimdScalarMathTest
26: [ RUN ] SimdScalarMathTest.copysign
26: [ OK ] SimdScalarMathTest.copysign (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPair
26: [ OK ] SimdScalarMathTest.invsqrtPair (1 ms)
26: [ RUN ] SimdScalarMathTest.inv
26: [ OK ] SimdScalarMathTest.inv (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrt
26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
26: [ RUN ] SimdScalarMathTest.log
26: [ OK ] SimdScalarMathTest.log (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2
26: [ OK ] SimdScalarMathTest.exp2 (0 ms)
26: [ RUN ] SimdScalarMathTest.exp
26: [ OK ] SimdScalarMathTest.exp (0 ms)
26: [ RUN ] SimdScalarMathTest.erf
26: [ OK ] SimdScalarMathTest.erf (0 ms)
26: [ RUN ] SimdScalarMathTest.erfc
26: [ OK ] SimdScalarMathTest.erfc (0 ms)
26: [ RUN ] SimdScalarMathTest.sincos
26: [ OK ] SimdScalarMathTest.sincos (0 ms)
26: [ RUN ] SimdScalarMathTest.sin
26: [ OK ] SimdScalarMathTest.sin (0 ms)
26: [ RUN ] SimdScalarMathTest.cos
26: [ OK ] SimdScalarMathTest.cos (0 ms)
26: [ RUN ] SimdScalarMathTest.tan
26: [ OK ] SimdScalarMathTest.tan (0 ms)
26: [ RUN ] SimdScalarMathTest.asin
26: [ OK ] SimdScalarMathTest.asin (0 ms)
26: [ RUN ] SimdScalarMathTest.acos
26: [ OK ] SimdScalarMathTest.acos (0 ms)
26: [ RUN ] SimdScalarMathTest.atan
26: [ OK ] SimdScalarMathTest.atan (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2
26: [ OK ] SimdScalarMathTest.atan2 (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrection
26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.invSingleAccuracy
26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.logSingleAccuracy
26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.expSingleAccuracy
26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
26: [----------] 37 tests from SimdScalarMathTest (5 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 86 tests from 3 test cases ran. (18 ms total)
26: [ PASSED ] 86 tests.
26/27 Test #26: SimdUnitTests .................... Passed 0.47 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/openmpi/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 6 tests from 6 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from CompatibilityHelper
27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles
27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms)
27: [----------] 1 test from CompatibilityHelper (0 ms total)
27:
27: [----------] 1 test from NotNullConstruction
27: [ RUN ] NotNullConstruction.Works
27: [ OK ] NotNullConstruction.Works (0 ms)
27: [----------] 1 test from NotNullConstruction (0 ms total)
27:
27: [----------] 1 test from NotNullCasting
27: [ RUN ] NotNullCasting.Works
27: [ OK ] NotNullCasting.Works (0 ms)
27: [----------] 1 test from NotNullCasting (0 ms total)
27:
27: [----------] 1 test from NotNullAssignment
27: [ RUN ] NotNullAssignment.Works
27: [ OK ] NotNullAssignment.Works (0 ms)
27: [----------] 1 test from NotNullAssignment (0 ms total)
27:
27: [----------] 1 test from MakeNotNull
27: [ RUN ] MakeNotNull.Works
27: [ OK ] MakeNotNull.Works (0 ms)
27: [----------] 1 test from MakeNotNull (0 ms total)
27:
27: [----------] 1 test from NotNull
27: [ RUN ] NotNull.WorksInContainers
27: [ OK ] NotNull.WorksInContainers (0 ms)
27: [----------] 1 test from NotNull (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 6 tests from 6 test cases ran. (2 ms total)
27: [ PASSED ] 6 tests.
27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.46 sec
100% tests passed, 0 tests failed out of 27
Label Time Summary:
GTest = 17.66 sec*proc (27 tests)
MpiTest = 2.21 sec*proc (3 tests)
UnitTest = 17.66 sec*proc (27 tests)
Total Test time (real) = 18.68 sec
/usr/bin/make -j4 -C build/openmpi-dp tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/external/googletest /<<PKGBUILDDIR>>/build/openmpi-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
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Scanning dependencies of target mdrunutility-test-shared
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
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Scanning dependencies of target gmock
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
[ 22%] Built target libgromacs_generated
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
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/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
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[ 23%] Built target mdrunutility-test-shared
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cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
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[ 80%] Built target libgromacs
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o
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cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi-printer.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata-xml.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/make_unique.cpp
Scanning dependencies of target testutils-test
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cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdlib-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/mdebin.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
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/usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/depend
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cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied-forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 84%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp:46:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied-forces/tests/electricfield.cpp:46:
/usr/include/c++/8/bits/stl_vector.h: In function 'void {anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/8/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::SettleTest_SatisfiesConstraints_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 84%] Built target applied-forces-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/listed-forces/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
Scanning dependencies of target listed-forces-test
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/usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed-forces/tests/bonded.cpp
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cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 85%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 85%] Built target listed-forces-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' {aka '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
updateGroupsCog.addCogs(globalAtomIndices, positions);
~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:173:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 86%] Built target mdlib-test
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 86%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 87%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
In file included from /usr/include/c++/8/map:61,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-internal.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:47,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:47:
/usr/include/c++/8/bits/stl_map.h: In function 'std::map<_Key, _Tp, _Compare, _Alloc>::map(std::initializer_list<std::pair<const _Key, _Tp> >, const _Compare&, const allocator_type&) [with _Key = gmx::BasicVector<int>; _Tp = t_complex; _Compare = std::less<gmx::BasicVector<int> >; _Alloc = std::allocator<std::pair<const gmx::BasicVector<int>, t_complex> >]':
/usr/include/c++/8/bits/stl_map.h:226:7: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
map(initializer_list<value_type> __l,
^~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp:343:1: note: parameter passing for argument of type 'std::initializer_list<std::pair<const gmx::BasicVector<int>, t_complex> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:97:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:165:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:174:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
};
^
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 88%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
vector(_InputIterator __first, _InputIterator __last,
^~~~~~
/usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:326:114: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates1(c_sampleCoordinatesFull.begin(), c_sampleCoordinatesFull.begin() + 1);
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:118: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates2(c_sampleCoordinatesFull.begin() + 1, c_sampleCoordinatesFull.begin() + 3);
^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:330:120: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
CoordinatesVector const c_sampleCoordinates13(c_sampleCoordinatesFull.begin() + 3, c_sampleCoordinatesFull.begin() + 16);
^
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 88%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void runTest(const gmx_gpu_info_t &gpuInfo,
^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void runTest(const gmx_gpu_info_t &gpuInfo,
^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:99:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:204:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 88%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 88%] Built target mdrunutility-mpi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
[ 89%] Built target ewald-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
Scanning dependencies of target onlinehelp-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 89%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void fillInputContents(ArrayRef < BasicVector < T>> inputRef,
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
void compareViews(ArrayRef<T> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
void compareViews(ArrayRef < BasicVector < T>> input,
^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:109:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 90%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 91%] Built target restraintpotential-test
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/8/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:517:16: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:461:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:467:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:489:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:176:5: note: in expansion of macro 'GMX_TEST_THROW_'
GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:494:5: note: in expansion of macro 'EXPECT_THROW_GMX'
EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp:50:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void {anonymous}::RVecTest_ConvertsImplicitlyFrom_rvec_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 91%] Built target math-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/bits/random.h:34,
from /usr/include/c++/8/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 91%] Built target table-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:119:40: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:131:39: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:142:38: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
}};
^
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 92%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
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make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 93%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 94%] Built target random-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 94%] Built target pull-test
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 94%] Built target fileio-test
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 95%] Built target options-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' {aka '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 95%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[ 97%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/gmxregex.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/openmpi-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/mpicxx.openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lm
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[100%] Built target utility-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
cd /<<PKGBUILDDIR>>/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp /<<PKGBUILDDIR>>/build/openmpi-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/openmpi-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/openmpi-dp'
(cd build/openmpi-dp ; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/openmpi-dp/lib \
OMPI_MCA_plm_rsh_agent=/bin/false \
OMPI_MCA_rmaps_base_oversubscribe=1 \
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/openmpi-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/openmpi-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/openmpi-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/openmpi-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/openmpi-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (14 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariants
1: [ OK ] ReferenceDataTest.HandlesVariants (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (33 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (1 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (1 ms)
1: [----------] 4 tests from XvgTests (6 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (55 ms total)
1: [ PASSED ] 59 tests.
1/27 Test #1: TestUtilsUnitTests ............... Passed 0.55 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "-host" "localhost" "/<<PKGBUILDDIR>>/build/openmpi-dp/bin/testutils-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (0 ms)
2: [----------] 1 test from MpiSelfTest (0 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (0 ms total)
2: [ PASSED ] 1 test.
2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.62 sec
test 3
Start 3: MdlibUnitTest
3: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/MdlibUnitTest.xml"
3: Test timeout computed to be: 30
3: [==========] Running 50 tests from 8 test cases.
3: [----------] Global test environment set-up.
3: [----------] 1 test from VerletBufferConstraintTest
3: [ RUN ] VerletBufferConstraintTest.EqualMasses
3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
3: [----------] 1 test from VerletBufferConstraintTest (0 ms total)
3:
3: [----------] 3 tests from PrintEbin
3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (2 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (1 ms)
3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages
3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms)
3: [----------] 3 tests from PrintEbin (4 ms total)
3:
3: [----------] 4 tests from ShakeTest
3: [ RUN ] ShakeTest.ConstrainsOneBond
3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
3: [----------] 4 tests from ShakeTest (0 ms total)
3:
3: [----------] 1 test from NullSignalTest
3: [ RUN ] NullSignalTest.NullSignallerWorks
3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
3: [----------] 1 test from NullSignalTest (0 ms total)
3:
3: [----------] 7 tests from SignalTest
3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
3: [----------] 7 tests from SignalTest (0 ms total)
3:
3: [----------] 9 tests from UpdateGroups
3: [ RUN ] UpdateGroups.ethaneUA
3: [ OK ] UpdateGroups.ethaneUA (1 ms)
3: [ RUN ] UpdateGroups.methane
3: [ OK ] UpdateGroups.methane (0 ms)
3: [ RUN ] UpdateGroups.ethane
3: [ OK ] UpdateGroups.ethane (0 ms)
3: [ RUN ] UpdateGroups.butaneUA
3: [ OK ] UpdateGroups.butaneUA (0 ms)
3: [ RUN ] UpdateGroups.waterThreeSite
3: [ OK ] UpdateGroups.waterThreeSite (0 ms)
3: [ RUN ] UpdateGroups.waterFourSite
3: [ OK ] UpdateGroups.waterFourSite (0 ms)
3: [ RUN ] UpdateGroups.fourAtomsWithSettle
3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
3: [ RUN ] UpdateGroups.waterFlexAngle
3: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
3: [ RUN ] UpdateGroups.twoMoltypes
3: [ OK ] UpdateGroups.twoMoltypes (0 ms)
3: [----------] 9 tests from UpdateGroups (1 ms total)
3:
3: [----------] 1 test from UpdateGroupsCog
3: [ RUN ] UpdateGroupsCog.ComputesCogs
3: [ OK ] UpdateGroupsCog.ComputesCogs (2 ms)
3: [----------] 1 test from UpdateGroupsCog (2 ms total)
3:
3: [----------] 24 tests from WithParameters/SettleTest
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (1 ms)
3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23
3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms)
3: [----------] 24 tests from WithParameters/SettleTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 50 tests from 8 test cases ran. (11 ms total)
3: [ PASSED ] 50 tests.
3/27 Test #3: MdlibUnitTest .................... Passed 0.50 sec
test 4
Start 4: AppliedForcesUnitTest
4: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/applied-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
4: Test timeout computed to be: 30
4: [==========] Running 3 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 3 tests from ElectricFieldTest
4: [ RUN ] ElectricFieldTest.Static
4: [ OK ] ElectricFieldTest.Static (0 ms)
4: [ RUN ] ElectricFieldTest.Oscillating
4: [ OK ] ElectricFieldTest.Oscillating (0 ms)
4: [ RUN ] ElectricFieldTest.Pulsed
4: [ OK ] ElectricFieldTest.Pulsed (0 ms)
4: [----------] 3 tests from ElectricFieldTest (1 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 3 tests from 1 test case ran. (2 ms total)
4: [ PASSED ] 3 tests.
4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.51 sec
test 5
Start 5: ListedForcesTest
5: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/listed-forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/ListedForcesTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 15 tests from 1 test case.
5: [----------] Global test environment set-up.
5: [----------] 15 tests from BondedTest
5: [ RUN ] BondedTest.BondAnglePbcNone
5: [ OK ] BondedTest.BondAnglePbcNone (0 ms)
5: [ RUN ] BondedTest.BondAnglePbcXy
5: [ OK ] BondedTest.BondAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.BondAnglePbcXyz
5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcNone
5: [ OK ] BondedTest.DihedralAnglePbcNone (1 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXy
5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms)
5: [ RUN ] BondedTest.DihedralAnglePbcXyz
5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcNo
5: [ OK ] BondedTest.IfuncBondsPbcNo (1 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXy
5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms)
5: [ RUN ] BondedTest.IfuncBondsPbcXyz
5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcNo
5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXy
5: [ OK ] BondedTest.IfuncAnglesPbcXy (1 ms)
5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ
5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo
5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (1 ms)
5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz
5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms)
5: [----------] 15 tests from BondedTest (5 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 15 tests from 1 test case ran. (5 ms total)
5: [ PASSED ] 15 tests.
5/27 Test #5: ListedForcesTest ................. Passed 0.60 sec
test 6
Start 6: CommandLineUnitTests
6: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/CommandLineUnitTests.xml"
6: Test timeout computed to be: 30
6: [==========] Running 55 tests from 6 test cases.
6: [----------] Global test environment set-up.
6: [----------] 3 tests from CommandLineHelpModuleTest
6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (2 ms)
6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms)
6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (5 ms)
6: [----------] 3 tests from CommandLineHelpModuleTest (9 ms total)
6:
6: [----------] 6 tests from CommandLineHelpWriterTest
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (2 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms)
6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
6: [----------] 6 tests from CommandLineHelpWriterTest (6 ms total)
6:
6: [----------] 6 tests from CommandLineModuleManagerTest
6: [ RUN ] CommandLineModuleManagerTest.RunsModule
6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms)
6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
6: [----------] 6 tests from CommandLineModuleManagerTest (3 ms total)
6:
6: [----------] 13 tests from CommandLineParserTest
6: [ RUN ] CommandLineParserTest.HandlesSingleValues
6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesString
6: [ OK ] CommandLineParserTest.HandlesString (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
6: [----------] 13 tests from CommandLineParserTest (2 ms total)
6:
6: [----------] 6 tests from CommandLineProgramContextTest
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
6:
6: [----------] 21 tests from ParseCommonArgsTest
6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (1 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (4 ms)
6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms)
6: [----------] 21 tests from ParseCommonArgsTest (14 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 55 tests from 6 test cases ran. (35 ms total)
6: [ PASSED ] 55 tests.
6/27 Test #6: CommandLineUnitTests ............. Passed 0.49 sec
test 7
Start 7: DomDecTests
7: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/DomDecTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 9 tests from 2 test cases.
7: [----------] Global test environment set-up.
7: [----------] 7 tests from HashedMap
7: [ RUN ] HashedMap.InsertsFinds
7: [ OK ] HashedMap.InsertsFinds (0 ms)
7: [ RUN ] HashedMap.NegativeKeysWork
7: [ OK ] HashedMap.NegativeKeysWork (0 ms)
7: [ RUN ] HashedMap.InsertsErases
7: [ OK ] HashedMap.InsertsErases (0 ms)
7: [ RUN ] HashedMap.InsertsOrAssigns
7: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
7: [ RUN ] HashedMap.Clears
7: [ OK ] HashedMap.Clears (0 ms)
7: [ RUN ] HashedMap.LinkedEntries
7: [ OK ] HashedMap.LinkedEntries (0 ms)
7: [ RUN ] HashedMap.ResizesTable
7: [ OK ] HashedMap.ResizesTable (0 ms)
7: [----------] 7 tests from HashedMap (1 ms total)
7:
7: [----------] 2 tests from LocalAtomSetManager
7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
7: [----------] 2 tests from LocalAtomSetManager (0 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 9 tests from 2 test cases ran. (1 ms total)
7: [ PASSED ] 9 tests.
7/27 Test #7: DomDecTests ...................... Passed 0.50 sec
test 8
Start 8: EwaldUnitTests
8: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/EwaldUnitTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 257 tests from 10 test cases.
8: [----------] Global test environment set-up.
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (14 ms)
8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms)
8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (17 ms total)
8:
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (19 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (17 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (17 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (19 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (18 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (19 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (20 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (21 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (28 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (47 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (33 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (27 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (26 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (27 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (24 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (20 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (21 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (21 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (21 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (25 ms)
8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (26 ms)
8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (566 ms total)
8:
8: [----------] 144 tests from SaneInput/PmeGatherTest
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (3 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (2 ms)
8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
8: [----------] 144 tests from SaneInput/PmeGatherTest (190 ms total)
8:
8: [----------] 16 tests from SaneInput/PmeSolveTest
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (9 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (11 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (7 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (11 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (11 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (7 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (6 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (8 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (7 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (4 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (4 ms)
8: [----------] 16 tests from SaneInput/PmeSolveTest (104 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (2 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (4 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (2 ms)
8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (27 ms total)
8:
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (7 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (8 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (7 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (46 ms total)
8:
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (7 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (7 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (8 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (7 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (4 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (4 ms)
8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (73 ms total)
8:
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (3 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (8 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms)
8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (8 ms)
8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (73 ms total)
8:
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (11 ms)
8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (12 ms)
8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (95 ms total)
8:
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (13 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (15 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (20 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (23 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (30 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (33 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (14 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (14 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (20 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (22 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (28 ms)
8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (35 ms)
8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (284 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 257 tests from 10 test cases ran. (1506 ms total)
8: [ PASSED ] 257 tests.
8/27 Test #8: EwaldUnitTests ................... Passed 2.10 sec
test 9
Start 9: FFTUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/FFTUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 14 tests from 4 test cases.
9: [----------] Global test environment set-up.
9: [----------] 2 tests from ManyFFTTest
9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (20 ms)
9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (34 ms)
9: [----------] 2 tests from ManyFFTTest (57 ms total)
9:
9: [----------] 1 test from FFTTest
9: [ RUN ] FFTTest.Real2DLength18_15Test
9: [ OK ] FFTTest.Real2DLength18_15Test (11 ms)
9: [----------] 1 test from FFTTest (12 ms total)
9:
9: [----------] 1 test from FFFTest3D
9: [ RUN ] FFFTest3D.Real5_6_9
9: [ OK ] FFFTest3D.Real5_6_9 (8 ms)
9: [----------] 1 test from FFFTest3D (10 ms total)
9:
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (2 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (3 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (5 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (5 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (16 ms)
9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (35 ms)
9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (72 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 14 tests from 4 test cases ran. (151 ms total)
9: [ PASSED ] 14 tests.
9/27 Test #9: FFTUnitTests ..................... Passed 0.61 sec
test 10
Start 10: GpuUtilsUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 60 tests from 19 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total)
10:
10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (1 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Swap
10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/0.Comparison
10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/0 (1 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Swap
10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/1.Comparison
10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Swap
10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/2.Comparison
10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total)
10:
10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Swap
10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
10: [ RUN ] HostAllocatorTestNoMem/3.Comparison
10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (1 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total)
10:
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
10:
10: [----------] 1 test from HostAllocatorUntypedTest
10: [ RUN ] HostAllocatorUntypedTest.Comparison
10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
10:
10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/0.Move
10: [ OK ] AllocatorTest/0.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/0 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/1.Move
10: [ OK ] AllocatorTest/1.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/1 (1 ms total)
10:
10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (2 ms)
10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/2.Move
10: [ OK ] AllocatorTest/2.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/2 (2 ms total)
10:
10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
10: [ RUN ] AllocatorTest/3.Move
10: [ OK ] AllocatorTest/3.Move (0 ms)
10: [----------] 4 tests from AllocatorTest/3 (1 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 60 tests from 19 test cases ran. (8 ms total)
10: [ PASSED ] 60 tests.
10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.52 sec
test 11
Start 11: HardwareUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/HardwareUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 4 tests from 1 test case.
11: [----------] Global test environment set-up.
11: [----------] 4 tests from HardwareTopologyTest
11: [ RUN ] HardwareTopologyTest.Execute
11: [ OK ] HardwareTopologyTest.Execute (37 ms)
11: [ RUN ] HardwareTopologyTest.HwlocExecute
11: [ OK ] HardwareTopologyTest.HwlocExecute (36 ms)
11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (33 ms)
11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (26 ms)
11: [----------] 4 tests from HardwareTopologyTest (132 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 4 tests from 1 test case ran. (132 ms total)
11: [ PASSED ] 4 tests.
11/27 Test #11: HardwareUnitTests ................ Passed 0.61 sec
test 12
Start 12: MathUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/MathUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 112 tests from 20 test cases.
12: [----------] Global test environment set-up.
12: [----------] 1 test from EmptyArrayRefWithPaddingTest
12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyArrayRefWithPaddingTest (1 ms total)
12:
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
12:
12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
12:
12: [----------] 6 tests from StructureSimilarityTest
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
12: [----------] 6 tests from StructureSimilarityTest (0 ms total)
12:
12: [----------] 21 tests from FunctionTest
12: [ RUN ] FunctionTest.StaticLog2
12: [ OK ] FunctionTest.StaticLog2 (1 ms)
12: [ RUN ] FunctionTest.Log2I32Bit
12: [ OK ] FunctionTest.Log2I32Bit (0 ms)
12: [ RUN ] FunctionTest.Log2I64Bit
12: [ OK ] FunctionTest.Log2I64Bit (1 ms)
12: [ RUN ] FunctionTest.GreatestCommonDivisor
12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
12: [ RUN ] FunctionTest.InvsqrtFloat
12: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
12: [ RUN ] FunctionTest.InvsqrtDouble
12: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
12: [ RUN ] FunctionTest.InvsqrtInteger
12: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
12: [ RUN ] FunctionTest.InvcbrtFloat
12: [ OK ] FunctionTest.InvcbrtFloat (1 ms)
12: [ RUN ] FunctionTest.InvcbrtDouble
12: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
12: [ RUN ] FunctionTest.InvcbrtInteger
12: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
12: [ RUN ] FunctionTest.SixthrootFloat
12: [ OK ] FunctionTest.SixthrootFloat (1 ms)
12: [ RUN ] FunctionTest.SixthrootDouble
12: [ OK ] FunctionTest.SixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.SixthrootInteger
12: [ OK ] FunctionTest.SixthrootInteger (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootFloat
12: [ OK ] FunctionTest.InvsixthrootFloat (1 ms)
12: [ RUN ] FunctionTest.InvsixthrootDouble
12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
12: [ RUN ] FunctionTest.InvsixthrootInteger
12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms)
12: [ RUN ] FunctionTest.Powers
12: [ OK ] FunctionTest.Powers (0 ms)
12: [ RUN ] FunctionTest.ErfInvFloat
12: [ OK ] FunctionTest.ErfInvFloat (0 ms)
12: [ RUN ] FunctionTest.ErfInvDouble
12: [ OK ] FunctionTest.ErfInvDouble (0 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
12: [----------] 21 tests from FunctionTest (9 ms total)
12:
12: [----------] 2 tests from InvertMatrixTest
12: [ RUN ] InvertMatrixTest.IdentityIsImpotent
12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertMatrixTest.ComputesInverse
12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
12: [----------] 2 tests from InvertMatrixTest (0 ms total)
12:
12: [----------] 2 tests from InvertBoxMatrixTest
12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanCopyAssign
12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/0.CanMoveAssign
12: [ OK ] PaddedVectorTest/0.CanMoveAssign (1 ms)
12: [ RUN ] PaddedVectorTest/0.CanSwap
12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/0 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanCopyAssign
12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanMoveAssign
12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/1.CanSwap
12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanCopyAssign
12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanMoveAssign
12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/2.CanSwap
12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanCopyAssign
12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanMoveAssign
12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/3.CanSwap
12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanCopyAssign
12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanMoveAssign
12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/4.CanSwap
12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/4 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanCopyAssign
12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanMoveAssign
12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/5.CanSwap
12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanCopyAssign
12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanMoveAssign
12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/6.CanSwap
12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanCopyAssign
12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanMoveAssign
12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/7.CanSwap
12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/7 (1 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanCopyAssign
12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanMoveAssign
12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/8.CanSwap
12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
12:
12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanCopyAssign
12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanMoveAssign
12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
12: [ RUN ] PaddedVectorTest/9.CanSwap
12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
12:
12: [----------] 33 tests from RVecTest
12: [ RUN ] RVecTest.CanBeStoredInVector
12: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAsMutable_rvec
12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Array
12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
12: [ RUN ] RVecTest.CanAddRVecToRvec
12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanAddAssignRVecToRvec
12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractRVecFromRvec
12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
12: [ RUN ] RVecTest.CanDotProductRVecByRvec
12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanCrossProductRVecByRvec
12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVecInplace
12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
12: [ RUN ] RVecTest.CanScaleRVec
12: [ OK ] RVecTest.CanScaleRVec (0 ms)
12: [ RUN ] RVecTest.CanDivideRVec
12: [ OK ] RVecTest.CanDivideRVec (0 ms)
12: [ RUN ] RVecTest.CanDoUnitvFromRVec
12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanSqLengthOfRVec
12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanLengthOfRVec
12: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToRVec
12: [ OK ] RVecTest.CanCastToRVec (0 ms)
12: [ RUN ] RVecTest.CanCastToDVec
12: [ OK ] RVecTest.CanCastToDVec (0 ms)
12: [ RUN ] RVecTest.CanLeftScalarMultiply
12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanRightScalarMultiply
12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
12: [ RUN ] RVecTest.CanGetUnitvFromRVec
12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
12: [ RUN ] RVecTest.CanGetSqLengthOfRVec
12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanGetLengthOfRVec
12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoCrossProductOfRVec
12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
12: [ RUN ] RVecTest.CanDoDotProductOfRVec
12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
12: [ RUN ] RVecTest.WorksAs_dvec_Reference
12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_ivec_Reference
12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
12: [ RUN ] RVecTest.WorksAs_rvec_Reference
12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
12: [ RUN ] RVecTest.CopyConstructorWorks
12: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
12: [ RUN ] RVecTest.CopyAssignmentWorks
12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
12: [ RUN ] RVecTest.MoveConstructorWorks
12: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
12: [ RUN ] RVecTest.MoveAssignmentWorks
12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
12: [----------] 33 tests from RVecTest (2 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 112 tests from 20 test cases ran. (15 ms total)
12: [ PASSED ] 112 tests.
12/27 Test #12: MathUnitTests .................... Passed 0.47 sec
test 13
Start 13: MdrunUtilityUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 17 tests from 1 test case.
13: [----------] Global test environment set-up.
13: [----------] 17 tests from ThreadAffinityTest
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
13: NOTE: Affinity setting failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms)
13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
13: NOTE: Affinity setting for 1/2 threads failed.
13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
13: [----------] 17 tests from ThreadAffinityTest (14 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 17 tests from 1 test case ran. (14 ms total)
13: [ PASSED ] 17 tests.
13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.50 sec
test 14
Start 14: MdrunUtilityMpiUnitTests
14: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/openmpi-dp/bin/mdrunutility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 13 tests from 2 test cases.
14: [----------] Global test environment set-up.
14: [----------] 6 tests from ThreadAffinityMultiRankTest
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (7 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (5 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (4 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (3 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (2 ms)
14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (2 ms)
14: [----------] 6 tests from ThreadAffinityMultiRankTest (25 ms total)
14:
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (4 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (2 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (3 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (3 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (4 ms)
14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (3 ms)
14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (30 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 13 tests from 2 test cases ran. (56 ms total)
14: [ PASSED ] 13 tests.
14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.84 sec
test 15
Start 15: OnlineHelpUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 22 tests from 4 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from TextTableFormatterTest
15: [ RUN ] TextTableFormatterTest.HandlesBasicCase
15: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesIndentation
15: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
15: [----------] 6 tests from TextTableFormatterTest (3 ms total)
15:
15: [----------] 3 tests from HelpManagerTest
15: [ RUN ] HelpManagerTest.HandlesRootTopic
15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms)
15: [ RUN ] HelpManagerTest.HandlesSubTopics
15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
15: [ RUN ] HelpManagerTest.HandlesInvalidTopics
15: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
15: [----------] 3 tests from HelpManagerTest (1 ms total)
15:
15: [----------] 2 tests from HelpTopicFormattingTest
15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
15:
15: [----------] 11 tests from HelpWriterContextTest
15: [ RUN ] HelpWriterContextTest.FormatsParagraphs
15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralText
15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsBulletList
15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
15: [ RUN ] HelpWriterContextTest.FormatsGridTable
15: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
15: [ RUN ] HelpWriterContextTest.FormatsTitles
15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
15: [----------] 11 tests from HelpWriterContextTest (4 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 22 tests from 4 test cases ran. (9 ms total)
15: [ PASSED ] 22 tests.
15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.53 sec
test 16
Start 16: OptionsUnitTests
16: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/OptionsUnitTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 110 tests from 18 test cases.
16: [----------] Global test environment set-up.
16: [----------] 5 tests from AbstractOptionStorageTest
16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms)
16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
16: [----------] 5 tests from AbstractOptionStorageTest (2 ms total)
16:
16: [----------] 8 tests from FileNameOptionTest
16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms)
16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
16: [----------] 8 tests from FileNameOptionTest (0 ms total)
16:
16: [----------] 15 tests from FileNameOptionManagerTest
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total)
16:
16: [----------] 1 test from OptionsTest
16: [ RUN ] OptionsTest.FailsOnNonsafeStorage
16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
16: [----------] 1 test from OptionsTest (0 ms total)
16:
16: [----------] 9 tests from OptionsAssignerTest
16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMissingValue
16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesExtraValue
16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesGroups
16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesSections
16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
16: [----------] 9 tests from OptionsAssignerTest (0 ms total)
16:
16: [----------] 4 tests from OptionsAssignerBooleanTest
16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
16: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
16:
16: [----------] 13 tests from OptionsAssignerIntegerTest
16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
16: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total)
16:
16: [----------] 5 tests from OptionsAssignerDoubleTest
16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (1 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
16:
16: [----------] 9 tests from OptionsAssignerStringTest
16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total)
16:
16: [----------] 6 tests from OptionsAssignerEnumTest
16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
16: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
16:
16: [----------] 8 tests from RepeatingOptionSectionTest
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total)
16:
16: [----------] 1 test from TimeUnitManagerTest
16: [ RUN ] TimeUnitManagerTest.BasicOperations
16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
16: [----------] 1 test from TimeUnitManagerTest (0 ms total)
16:
16: [----------] 4 tests from TimeUnitBehaviorTest
16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
16: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
16:
16: [----------] 2 tests from TreeValueSupportAssignTest
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
16:
16: [----------] 1 test from TreeValueSupportAssignErrorTest
16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
16:
16: [----------] 5 tests from TreeValueSupportCheckTest
16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
16:
16: [----------] 6 tests from TreeValueSupportAdjustTest
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms)
16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (1 ms)
16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
16: [----------] 6 tests from TreeValueSupportAdjustTest (2 ms total)
16:
16: [----------] 8 tests from TreeValueSupportTest
16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsInt64Option
16: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsStringOption
16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsFloatOption
16: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
16: [ RUN ] TreeValueSupportTest.SupportsEnumOption
16: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
16: [----------] 8 tests from TreeValueSupportTest (3 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 110 tests from 18 test cases ran. (13 ms total)
16: [ PASSED ] 110 tests.
16/27 Test #16: OptionsUnitTests ................. Passed 0.51 sec
test 17
Start 17: RandomUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/RandomUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 44 tests from 10 test cases.
17: [----------] Global test environment set-up.
17: [----------] 4 tests from ExponentialDistributionTest
17: [ RUN ] ExponentialDistributionTest.Output
17: [ OK ] ExponentialDistributionTest.Output (1 ms)
17: [ RUN ] ExponentialDistributionTest.Logical
17: [ OK ] ExponentialDistributionTest.Logical (0 ms)
17: [ RUN ] ExponentialDistributionTest.Reset
17: [ OK ] ExponentialDistributionTest.Reset (0 ms)
17: [ RUN ] ExponentialDistributionTest.AltParam
17: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
17:
17: [----------] 4 tests from GammaDistributionTest
17: [ RUN ] GammaDistributionTest.Output
17: [ OK ] GammaDistributionTest.Output (1 ms)
17: [ RUN ] GammaDistributionTest.Logical
17: [ OK ] GammaDistributionTest.Logical (0 ms)
17: [ RUN ] GammaDistributionTest.Reset
17: [ OK ] GammaDistributionTest.Reset (0 ms)
17: [ RUN ] GammaDistributionTest.AltParam
17: [ OK ] GammaDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from GammaDistributionTest (1 ms total)
17:
17: [----------] 4 tests from NormalDistributionTest
17: [ RUN ] NormalDistributionTest.Output
17: [ OK ] NormalDistributionTest.Output (0 ms)
17: [ RUN ] NormalDistributionTest.Logical
17: [ OK ] NormalDistributionTest.Logical (0 ms)
17: [ RUN ] NormalDistributionTest.Reset
17: [ OK ] NormalDistributionTest.Reset (0 ms)
17: [ RUN ] NormalDistributionTest.AltParam
17: [ OK ] NormalDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from NormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from SeedTest
17: [ RUN ] SeedTest.makeRandomSeed
17: [ OK ] SeedTest.makeRandomSeed (0 ms)
17: [----------] 1 test from SeedTest (0 ms total)
17:
17: [----------] 6 tests from TabulatedNormalDistributionTest
17: [ RUN ] TabulatedNormalDistributionTest.Output14
17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Output16
17: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Logical
17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.Reset
17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
17: [ RUN ] TabulatedNormalDistributionTest.AltParam
17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
17: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total)
17:
17: [----------] 1 test from TabulatedNormalDistributionTableTest
17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (8 ms)
17: [----------] 1 test from TabulatedNormalDistributionTableTest (8 ms total)
17:
17: [----------] 6 tests from ThreeFry2x64Test
17: [ RUN ] ThreeFry2x64Test.Logical
17: [ OK ] ThreeFry2x64Test.Logical (0 ms)
17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms)
17: [ RUN ] ThreeFry2x64Test.Reseed
17: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
17: [ RUN ] ThreeFry2x64Test.Discard
17: [ OK ] ThreeFry2x64Test.Discard (0 ms)
17: [ RUN ] ThreeFry2x64Test.InvalidCounter
17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
17: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
17:
17: [----------] 4 tests from UniformIntDistributionTest
17: [ RUN ] UniformIntDistributionTest.Output
17: [ OK ] UniformIntDistributionTest.Output (0 ms)
17: [ RUN ] UniformIntDistributionTest.Logical
17: [ OK ] UniformIntDistributionTest.Logical (0 ms)
17: [ RUN ] UniformIntDistributionTest.Reset
17: [ OK ] UniformIntDistributionTest.Reset (0 ms)
17: [ RUN ] UniformIntDistributionTest.AltParam
17: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
17: [----------] 4 tests from UniformIntDistributionTest (1 ms total)
17:
17: [----------] 5 tests from UniformRealDistributionTest
17: [ RUN ] UniformRealDistributionTest.GenerateCanonical
17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Output
17: [ OK ] UniformRealDistributionTest.Output (0 ms)
17: [ RUN ] UniformRealDistributionTest.Logical
17: [ OK ] UniformRealDistributionTest.Logical (0 ms)
17: [ RUN ] UniformRealDistributionTest.Reset
17: [ OK ] UniformRealDistributionTest.Reset (0 ms)
17: [ RUN ] UniformRealDistributionTest.AltParam
17: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
17: [----------] 5 tests from UniformRealDistributionTest (1 ms total)
17:
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms)
17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 44 tests from 10 test cases ran. (18 ms total)
17: [ PASSED ] 44 tests.
17/27 Test #17: RandomUnitTests .................. Passed 0.56 sec
test 18
Start 18: RestraintTests
18: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/RestraintTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 1 test from 1 test case.
18: [----------] Global test environment set-up.
18: [----------] 1 test from RestraintManager
18: [ RUN ] RestraintManager.restraintList
18: [ OK ] RestraintManager.restraintList (0 ms)
18: [----------] 1 test from RestraintManager (0 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 1 test from 1 test case ran. (0 ms total)
18: [ PASSED ] 1 test.
18/27 Test #18: RestraintTests ................... Passed 0.47 sec
test 19
Start 19: TableUnitTests
19: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/TableUnitTests.xml"
19: Test timeout computed to be: 30
19: [==========] Running 16 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (7 ms)
19: [ RUN ] SplineTableTest/0.Sinc
19: [ OK ] SplineTableTest/0.Sinc (3 ms)
19: [ RUN ] SplineTableTest/0.LJ12
19: [ OK ] SplineTableTest/0.LJ12 (97 ms)
19: [ RUN ] SplineTableTest/0.PmeCorrection
19: [ OK ] SplineTableTest/0.PmeCorrection (5 ms)
19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (4 ms)
19: [ RUN ] SplineTableTest/0.TwoFunctions
19: [ OK ] SplineTableTest/0.TwoFunctions (239 ms)
19: [ RUN ] SplineTableTest/0.ThreeFunctions
19: [ OK ] SplineTableTest/0.ThreeFunctions (224 ms)
19: [----------] 8 tests from SplineTableTest/0 (581 ms total)
19:
19: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
19: [ RUN ] SplineTableTest/1.Sinc
19: [ OK ] SplineTableTest/1.Sinc (6 ms)
19: [ RUN ] SplineTableTest/1.LJ12
19: [ OK ] SplineTableTest/1.LJ12 (283 ms)
19: [ RUN ] SplineTableTest/1.PmeCorrection
19: [ OK ] SplineTableTest/1.PmeCorrection (6 ms)
19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (5 ms)
19: [ RUN ] SplineTableTest/1.TwoFunctions
19: [ OK ] SplineTableTest/1.TwoFunctions (590 ms)
19: [ RUN ] SplineTableTest/1.ThreeFunctions
19: [ OK ] SplineTableTest/1.ThreeFunctions (600 ms)
19: [----------] 8 tests from SplineTableTest/1 (1499 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 16 tests from 2 test cases ran. (2080 ms total)
19: [ PASSED ] 16 tests.
19/27 Test #19: TableUnitTests ................... Passed 2.58 sec
test 20
Start 20: TaskAssignmentUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 3 tests from 1 test case.
20: [----------] Global test environment set-up.
20: [----------] 3 tests from GpuIdStringHandlingTest
20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork
20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid
20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms)
20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow
20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms)
20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 3 tests from 1 test case ran. (1 ms total)
20: [ PASSED ] 3 tests.
20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.47 sec
test 21
Start 21: UtilityUnitTests
21: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/UtilityUnitTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 325 tests from 52 test cases.
21: [----------] Global test environment set-up.
21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/0.Move
21: [ OK ] AllocatorTest/0.Move (0 ms)
21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/0 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/1.Move
21: [ OK ] AllocatorTest/1.Move (0 ms)
21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/1 (3 ms total)
21:
21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/2.Move
21: [ OK ] AllocatorTest/2.Move (0 ms)
21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/2 (1 ms total)
21:
21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/3.Move
21: [ OK ] AllocatorTest/3.Move (0 ms)
21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/3 (2 ms total)
21:
21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (2 ms)
21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/4.Move
21: [ OK ] AllocatorTest/4.Move (0 ms)
21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/4 (3 ms total)
21:
21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (2 ms)
21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
21: [ RUN ] AllocatorTest/5.Move
21: [ OK ] AllocatorTest/5.Move (0 ms)
21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
21: [----------] 5 tests from AllocatorTest/5 (3 ms total)
21:
21: [----------] 1 test from AllocatorUntypedTest
21: [ RUN ] AllocatorUntypedTest.Comparison
21: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
21: [----------] 1 test from AllocatorUntypedTest (0 ms total)
21:
21: [----------] 1 test from EmptyArrayRefTest
21: [ RUN ] EmptyArrayRefTest.IsEmpty
21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyArrayRefTest (0 ms total)
21:
21: [----------] 1 test from EmptyConstArrayRefTest
21: [ RUN ] EmptyConstArrayRefTest.IsEmpty
21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (1 ms)
21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/0 (2 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/1 (2 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/2 (2 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/3 (2 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/4 (2 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/5 (3 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (1 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/10 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
21:
21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
21: [----------] 9 tests from ArrayRefTest/19 (0 ms total)
21:
21: [----------] 4 tests from KeyValueTreeSerializerTest
21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms)
21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
21: [----------] 4 tests from KeyValueTreeSerializerTest (2 ms total)
21:
21: [----------] 6 tests from TreeValueTransformTest
21: [ RUN ] TreeValueTransformTest.SimpleTransforms
21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms)
21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromString
21: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms)
21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms)
21: [ RUN ] TreeValueTransformTest.ScopedTransformRules
21: [ OK ] TreeValueTransformTest.ScopedTransformRules (1 ms)
21: [----------] 6 tests from TreeValueTransformTest (3 ms total)
21:
21: [----------] 1 test from TreeValueTransformErrorTest
21: [ RUN ] TreeValueTransformErrorTest.ConversionError
21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
21:
21: [----------] 2 tests from RegexBasicTest
21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported
21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms)
21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported
21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (2 ms)
21: [----------] 2 tests from RegexBasicTest (3 ms total)
21:
21: [----------] 5 tests from LoggerTest
21: [ RUN ] LoggerTest.EmptyLoggerWorks
21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
21: [ RUN ] LoggerTest.LogsToStream
21: [ OK ] LoggerTest.LogsToStream (0 ms)
21: [ RUN ] LoggerTest.LogsToFile
21: [ OK ] LoggerTest.LogsToFile (1 ms)
21: [ RUN ] LoggerTest.LevelFilteringWorks
21: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
21: [ RUN ] LoggerTest.LogsToMultipleStreams
21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
21: [----------] 5 tests from LoggerTest (2 ms total)
21:
21: [----------] 4 tests from MutexBasicTest
21: [ RUN ] MutexBasicTest.CanBeMade
21: [ OK ] MutexBasicTest.CanBeMade (0 ms)
21: [ RUN ] MutexBasicTest.CanBeLocked
21: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeTryLocked
21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
21: [----------] 4 tests from MutexBasicTest (0 ms total)
21:
21: [----------] 3 tests from MutexTaskTest
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
21: [----------] 3 tests from MutexTaskTest (2 ms total)
21:
21: [----------] 4 tests from PathTest
21: [ RUN ] PathTest.StripSourcePrefixWorks
21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks
21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathWorks
21: [ OK ] PathTest.GetParentPathWorks (0 ms)
21: [ RUN ] PathTest.GetParentPathAndBasenameWorks
21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms)
21: [----------] 4 tests from PathTest (0 ms total)
21:
21: [----------] 2 tests from PhysicalNodeCommunicatorTest
21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
21:
21: [----------] 7 tests from StringUtilityTest
21: [ RUN ] StringUtilityTest.StartsWith
21: [ OK ] StringUtilityTest.StartsWith (0 ms)
21: [ RUN ] StringUtilityTest.EndsWith
21: [ OK ] StringUtilityTest.EndsWith (0 ms)
21: [ RUN ] StringUtilityTest.StripSuffixIfPresent
21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
21: [ RUN ] StringUtilityTest.StripString
21: [ OK ] StringUtilityTest.StripString (0 ms)
21: [ RUN ] StringUtilityTest.SplitString
21: [ OK ] StringUtilityTest.SplitString (1 ms)
21: [ RUN ] StringUtilityTest.SplitDelimitedString
21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
21: [----------] 7 tests from StringUtilityTest (2 ms total)
21:
21: [----------] 2 tests from FormatStringTest
21: [ RUN ] FormatStringTest.HandlesBasicFormatting
21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
21: [ RUN ] FormatStringTest.HandlesLongStrings
21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
21: [----------] 2 tests from FormatStringTest (0 ms total)
21:
21: [----------] 1 test from StringFormatterTest
21: [ RUN ] StringFormatterTest.HandlesBasicFormatting
21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
21: [----------] 1 test from StringFormatterTest (0 ms total)
21:
21: [----------] 1 test from formatAndJoinTest
21: [ RUN ] formatAndJoinTest.Works
21: [ OK ] formatAndJoinTest.Works (0 ms)
21: [----------] 1 test from formatAndJoinTest (0 ms total)
21:
21: [----------] 1 test from JoinStringsTest
21: [ RUN ] JoinStringsTest.Works
21: [ OK ] JoinStringsTest.Works (0 ms)
21: [----------] 1 test from JoinStringsTest (0 ms total)
21:
21: [----------] 6 tests from ReplaceAllTest
21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesNoMatches
21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
21: [----------] 6 tests from ReplaceAllTest (0 ms total)
21:
21: [----------] 10 tests from TextLineWrapperTest
21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectly
21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (1 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndent
21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
21: [----------] 10 tests from TextLineWrapperTest (2 ms total)
21:
21: [----------] 6 tests from TextWriterTest
21: [ RUN ] TextWriterTest.WritesLines
21: [ OK ] TextWriterTest.WritesLines (0 ms)
21: [ RUN ] TextWriterTest.WritesLinesInParts
21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
21: [ RUN ] TextWriterTest.WritesWrappedLines
21: [ OK ] TextWriterTest.WritesWrappedLines (1 ms)
21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
21: [ RUN ] TextWriterTest.TracksNewlines
21: [ OK ] TextWriterTest.TracksNewlines (0 ms)
21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
21: [----------] 6 tests from TextWriterTest (1 ms total)
21:
21: [----------] 1 test from TypeTraitsTest
21: [ RUN ] TypeTraitsTest.IsIntegralConstant
21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
21: [----------] 1 test from TypeTraitsTest (0 ms total)
21:
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
21:
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
21:
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total)
21:
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (1 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
21:
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (1 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (2 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 325 tests from 52 test cases ran. (63 ms total)
21: [ PASSED ] 325 tests.
21/27 Test #21: UtilityUnitTests ................. Passed 0.59 sec
test 22
Start 22: UtilityMpiUnitTests
22: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "-host" "localhost" "/<<PKGBUILDDIR>>/build/openmpi-dp/bin/utility-mpi-test" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 2 tests from 1 test case.
22: [----------] Global test environment set-up.
22: [----------] 2 tests from PhysicalNodeCommunicatorTest
22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (1 ms)
22: [----------] 2 tests from PhysicalNodeCommunicatorTest (5 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 2 tests from 1 test case ran. (5 ms total)
22: [ PASSED ] 2 tests.
22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.72 sec
test 23
Start 23: FileIOTests
23: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/FileIOTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 17 tests from 4 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from FileMD5Test
23: [ RUN ] FileMD5Test.CanComputeMD5
23: [ OK ] FileMD5Test.CanComputeMD5 (7 ms)
23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
23: [----------] 2 tests from FileMD5Test (10 ms total)
23:
23: [----------] 9 tests from ReadTest
23: [ RUN ] ReadTest.get_eint_ReadsInteger
23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (1 ms)
23: [ RUN ] ReadTest.get_eint_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_eint64_ReadsInteger
23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side '0.8' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
23: [ RUN ] ReadTest.get_eint64_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not an
23: integer value
23:
23:
23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsInteger
23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
23: [ RUN ] ReadTest.get_ereal_ReadsFloat
23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
23: [ RUN ] ReadTest.get_ereal_WarnsAboutString
23:
23: ERROR 1 [file unknown, line 0]:
23: Right hand side 'hello' for parameter 'test' in parameter file is not a
23: real value
23:
23:
23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
23: [----------] 9 tests from ReadTest (4 ms total)
23:
23: [----------] 2 tests from TngTest
23: [ RUN ] TngTest.CanOpenTngFile
23: [ OK ] TngTest.CanOpenTngFile (0 ms)
23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
23: [----------] 2 tests from TngTest (1 ms total)
23:
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (4 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (15 ms)
23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (25 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 17 tests from 4 test cases ran. (44 ms total)
23: [ PASSED ] 17 tests.
23/27 Test #23: FileIOTests ...................... Passed 0.51 sec
test 24
Start 24: PullTest
24: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/PullTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 5 tests from 1 test case.
24: [----------] Global test environment set-up.
24: [----------] 5 tests from PullTest
24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
24: [----------] 5 tests from PullTest (1 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 5 tests from 1 test case ran. (2 ms total)
24: [ PASSED ] 5 tests.
24/27 Test #24: PullTest ......................... Passed 0.44 sec
test 25
Start 25: AwhTest
25: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/AwhTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 12 tests from 4 test cases.
25: [----------] Global test environment set-up.
25: [----------] 1 test from BiasTest
25: [ RUN ] BiasTest.DetectsCovering
25: [ OK ] BiasTest.DetectsCovering (2 ms)
25: [----------] 1 test from BiasTest (3 ms total)
25:
25: [----------] 1 test from gridTest
25: [ RUN ] gridTest.neighborhood
25: [ OK ] gridTest.neighborhood (5 ms)
25: [----------] 1 test from gridTest (5 ms total)
25:
25: [----------] 8 tests from WithParameters/BiasTest
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (2 ms)
25: [----------] 8 tests from WithParameters/BiasTest (16 ms total)
25:
25: [----------] 2 tests from WithParameters/BiasStateTest
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms)
25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms)
25: [----------] 2 tests from WithParameters/BiasStateTest (2 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 12 tests from 4 test cases ran. (28 ms total)
25: [ PASSED ] 12 tests.
25/27 Test #25: AwhTest .......................... Passed 0.45 sec
test 26
Start 26: SimdUnitTests
26: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/SimdUnitTests.xml"
26: Test timeout computed to be: 30
26: [==========] Running 86 tests from 3 test cases.
26: [----------] Global test environment set-up.
26: [----------] 41 tests from SimdScalarTest
26: [ RUN ] SimdScalarTest.load
26: [ OK ] SimdScalarTest.load (0 ms)
26: [ RUN ] SimdScalarTest.loadU
26: [ OK ] SimdScalarTest.loadU (0 ms)
26: [ RUN ] SimdScalarTest.store
26: [ OK ] SimdScalarTest.store (0 ms)
26: [ RUN ] SimdScalarTest.storeU
26: [ OK ] SimdScalarTest.storeU (0 ms)
26: [ RUN ] SimdScalarTest.setZero
26: [ OK ] SimdScalarTest.setZero (0 ms)
26: [ RUN ] SimdScalarTest.andNot
26: [ OK ] SimdScalarTest.andNot (0 ms)
26: [ RUN ] SimdScalarTest.fma
26: [ OK ] SimdScalarTest.fma (0 ms)
26: [ RUN ] SimdScalarTest.fms
26: [ OK ] SimdScalarTest.fms (0 ms)
26: [ RUN ] SimdScalarTest.fnma
26: [ OK ] SimdScalarTest.fnma (0 ms)
26: [ RUN ] SimdScalarTest.fnms
26: [ OK ] SimdScalarTest.fnms (0 ms)
26: [ RUN ] SimdScalarTest.maskAdd
26: [ OK ] SimdScalarTest.maskAdd (0 ms)
26: [ RUN ] SimdScalarTest.maskzMul
26: [ OK ] SimdScalarTest.maskzMul (0 ms)
26: [ RUN ] SimdScalarTest.maskzFma
26: [ OK ] SimdScalarTest.maskzFma (0 ms)
26: [ RUN ] SimdScalarTest.abs
26: [ OK ] SimdScalarTest.abs (0 ms)
26: [ RUN ] SimdScalarTest.max
26: [ OK ] SimdScalarTest.max (0 ms)
26: [ RUN ] SimdScalarTest.min
26: [ OK ] SimdScalarTest.min (0 ms)
26: [ RUN ] SimdScalarTest.round
26: [ OK ] SimdScalarTest.round (0 ms)
26: [ RUN ] SimdScalarTest.trunc
26: [ OK ] SimdScalarTest.trunc (0 ms)
26: [ RUN ] SimdScalarTest.reduce
26: [ OK ] SimdScalarTest.reduce (0 ms)
26: [ RUN ] SimdScalarTest.testBits
26: [ OK ] SimdScalarTest.testBits (0 ms)
26: [ RUN ] SimdScalarTest.anyTrue
26: [ OK ] SimdScalarTest.anyTrue (0 ms)
26: [ RUN ] SimdScalarTest.selectByMask
26: [ OK ] SimdScalarTest.selectByMask (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMask
26: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
26: [ RUN ] SimdScalarTest.blend
26: [ OK ] SimdScalarTest.blend (0 ms)
26: [ RUN ] SimdScalarTest.cvtR2I
26: [ OK ] SimdScalarTest.cvtR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvttR2I
26: [ OK ] SimdScalarTest.cvttR2I (0 ms)
26: [ RUN ] SimdScalarTest.cvtI2R
26: [ OK ] SimdScalarTest.cvtI2R (1 ms)
26: [ RUN ] SimdScalarTest.cvtF2D
26: [ OK ] SimdScalarTest.cvtF2D (0 ms)
26: [ RUN ] SimdScalarTest.cvtD2D
26: [ OK ] SimdScalarTest.cvtD2D (0 ms)
26: [ RUN ] SimdScalarTest.loadI
26: [ OK ] SimdScalarTest.loadI (0 ms)
26: [ RUN ] SimdScalarTest.loadUI
26: [ OK ] SimdScalarTest.loadUI (0 ms)
26: [ RUN ] SimdScalarTest.storeI
26: [ OK ] SimdScalarTest.storeI (0 ms)
26: [ RUN ] SimdScalarTest.storeUI
26: [ OK ] SimdScalarTest.storeUI (0 ms)
26: [ RUN ] SimdScalarTest.andNotI
26: [ OK ] SimdScalarTest.andNotI (0 ms)
26: [ RUN ] SimdScalarTest.testBitsI
26: [ OK ] SimdScalarTest.testBitsI (0 ms)
26: [ RUN ] SimdScalarTest.selectByMaskI
26: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
26: [ RUN ] SimdScalarTest.selectByNotMaskI
26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
26: [ RUN ] SimdScalarTest.blendI
26: [ OK ] SimdScalarTest.blendI (0 ms)
26: [ RUN ] SimdScalarTest.cvtB2IB
26: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
26: [ RUN ] SimdScalarTest.cvtIB2B
26: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
26: [ RUN ] SimdScalarTest.expandScalarsToTriplets
26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
26: [----------] 41 tests from SimdScalarTest (13 ms total)
26:
26: [----------] 8 tests from SimdScalarUtilTest
26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
26: [----------] 8 tests from SimdScalarUtilTest (3 ms total)
26:
26: [----------] 37 tests from SimdScalarMathTest
26: [ RUN ] SimdScalarMathTest.copysign
26: [ OK ] SimdScalarMathTest.copysign (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPair
26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
26: [ RUN ] SimdScalarMathTest.inv
26: [ OK ] SimdScalarMathTest.inv (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrt
26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
26: [ RUN ] SimdScalarMathTest.log
26: [ OK ] SimdScalarMathTest.log (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2
26: [ OK ] SimdScalarMathTest.exp2 (0 ms)
26: [ RUN ] SimdScalarMathTest.exp
26: [ OK ] SimdScalarMathTest.exp (0 ms)
26: [ RUN ] SimdScalarMathTest.erf
26: [ OK ] SimdScalarMathTest.erf (0 ms)
26: [ RUN ] SimdScalarMathTest.erfc
26: [ OK ] SimdScalarMathTest.erfc (0 ms)
26: [ RUN ] SimdScalarMathTest.sincos
26: [ OK ] SimdScalarMathTest.sincos (0 ms)
26: [ RUN ] SimdScalarMathTest.sin
26: [ OK ] SimdScalarMathTest.sin (0 ms)
26: [ RUN ] SimdScalarMathTest.cos
26: [ OK ] SimdScalarMathTest.cos (0 ms)
26: [ RUN ] SimdScalarMathTest.tan
26: [ OK ] SimdScalarMathTest.tan (0 ms)
26: [ RUN ] SimdScalarMathTest.asin
26: [ OK ] SimdScalarMathTest.asin (0 ms)
26: [ RUN ] SimdScalarMathTest.acos
26: [ OK ] SimdScalarMathTest.acos (0 ms)
26: [ RUN ] SimdScalarMathTest.atan
26: [ OK ] SimdScalarMathTest.atan (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2
26: [ OK ] SimdScalarMathTest.atan2 (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrection
26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.invSingleAccuracy
26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.logSingleAccuracy
26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.expSingleAccuracy
26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
26: [----------] 37 tests from SimdScalarMathTest (2 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 86 tests from 3 test cases ran. (19 ms total)
26: [ PASSED ] 86 tests.
26/27 Test #26: SimdUnitTests .................... Passed 0.52 sec
test 27
Start 27: CompatibilityHelpersTests
27: Test command: /<<PKGBUILDDIR>>/build/openmpi-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/openmpi-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 6 tests from 6 test cases.
27: [----------] Global test environment set-up.
27: [----------] 1 test from CompatibilityHelper
27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles
27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms)
27: [----------] 1 test from CompatibilityHelper (0 ms total)
27:
27: [----------] 1 test from NotNullConstruction
27: [ RUN ] NotNullConstruction.Works
27: [ OK ] NotNullConstruction.Works (0 ms)
27: [----------] 1 test from NotNullConstruction (1 ms total)
27:
27: [----------] 1 test from NotNullCasting
27: [ RUN ] NotNullCasting.Works
27: [ OK ] NotNullCasting.Works (0 ms)
27: [----------] 1 test from NotNullCasting (0 ms total)
27:
27: [----------] 1 test from NotNullAssignment
27: [ RUN ] NotNullAssignment.Works
27: [ OK ] NotNullAssignment.Works (0 ms)
27: [----------] 1 test from NotNullAssignment (1 ms total)
27:
27: [----------] 1 test from MakeNotNull
27: [ RUN ] MakeNotNull.Works
27: [ OK ] MakeNotNull.Works (0 ms)
27: [----------] 1 test from MakeNotNull (0 ms total)
27:
27: [----------] 1 test from NotNull
27: [ RUN ] NotNull.WorksInContainers
27: [ OK ] NotNull.WorksInContainers (0 ms)
27: [----------] 1 test from NotNull (0 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 6 tests from 6 test cases ran. (4 ms total)
27: [ PASSED ] 6 tests.
27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.47 sec
100% tests passed, 0 tests failed out of 27
Label Time Summary:
GTest = 18.24 sec*proc (27 tests)
MpiTest = 2.19 sec*proc (3 tests)
UnitTest = 18.24 sec*proc (27 tests)
Total Test time (real) = 19.33 sec
touch build-openmpi
dh_testdir
dh_testroot
dh_prep -pgromacs
dh_installdirs -pgromacs
/usr/bin/make -j4 -C build/basic install DESTDIR=/<<PKGBUILDDIR>>/debian/gromacs
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic/CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build
[ 0%] Built target lmfit_objlib
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 2%] Built target tng_io_obj
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
[ 6%] Built target libgromacs_external
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 6%] Built target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 7%] Built target view_objlib
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 24%] Built target libgromacs_generated
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
[ 25%] Built target mdrun_test_objlib
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/share/template /<<PKGBUILDDIR>>/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target template
[100%] Built target gmx
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
/usr/bin/make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-morph.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-make_edi.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-lie.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-report-methods.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-helixorient.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-xpm2ps.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-grompp.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-solvate.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-tune_pme.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-tcaf.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-freevolume.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-dielectric.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-nmr.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-current.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-velacc.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-pairdist.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-dyecoupl.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-genion.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-gangle.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-check.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-disre.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-editconf.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-nmens.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-nmeig.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rms.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-msd.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-sorient.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-hydorder.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-mdrun.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-trjconv.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-wham.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-dyndom.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-helix.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-trjorder.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-pme_error.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-convert-tpr.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-h2order.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-gyrate.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rotmat.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rotacf.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-saxs.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-trajectory.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-sans.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-vanhove.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-cluster.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rama.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-saltbr.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-help.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-mdmat.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-potential.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-density.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-polystat.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-genconf.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-anaeig.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-dos.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-trjcat.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-analyze.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-awh.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-principal.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-genrestr.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-insert-molecules.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-bundle.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-energy.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-make_ndx.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-view.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-mindist.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-pdb2gmx.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-traj.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rdf.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-sasa.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-hbond.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-clustsize.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-select.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-dipoles.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-covar.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-densmap.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rmsdist.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-distance.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-chi.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-enemat.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-bar.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-spol.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-confrms.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-rmsf.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-eneconv.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-order.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-filter.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-x2top.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-sham.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-sigeps.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-dump.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-angle.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-anadock.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-wheel.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-do_dssp.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-spatial.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/man/man1/gmx-densorder.1
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/README.tutor
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/README_FreeEnergyModifications.txt
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/random.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/xlateat.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/methanol.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/1propanol.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ethanol.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffoplsaa.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/edissoc.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/flexwat-ferguson.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/table6-9.xvg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/table6-10.xvg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/elements.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ha-shift.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/spc216.gro
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffG43a1.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/README
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/refi_aa.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/dgsolv.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/specbond.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/export.dlg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/sw.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/defselection.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/residues.xml
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/electroneg.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/atommass.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/methanol.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ps.m2p
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/surface.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/tip5p.gro
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/popc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/dppc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/nsfactor.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffG53a5.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tips3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/cmap.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/vdw-msms.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffG53a6.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/atom_nom.tbl
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/tip4p.gro
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/table6-12.xvg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/residues.dtd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/vdwradii.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffoplsaa-n.tst
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffG43a2.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/ff_dum.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos53a6.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/bonds.dlg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/flexspce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ffG45a3.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/residuetypes.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/sfactor.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber94.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/co-shift.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/cb-shift.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ca-shift.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber99sb.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/table6-8.xvg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/phbres.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/rna.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip5p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip4pew.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/urea.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/aminoacids.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/amber96.ff/dna.arn
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/table6-11.xvg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/ss.map
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ions.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffnonbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.r2b
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ffbonded.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.hdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spce.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.vsd
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/atomtypes.atp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.c.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip4p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/ff_dum.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.n.tdb
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.doc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/aminoacids.rtp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/forcefield.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/watermodels.dat
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/tip3p.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/gromos45a3.ff/spc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/top/flexspc.itp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/template/CMakeLists.txt
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/template/README
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/template/template.cpp
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/template/Makefile.pkg
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/gromacs/template/cmake/FindGROMACS.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/bin/GMXRC
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/bin/GMXRC.bash
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/bin/GMXRC.zsh
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/bin/GMXRC.csh
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/bin/demux.pl
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/bin/xplor2gmx.pl
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/analysisdata.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/options.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/random.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/selection.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/trajectoryanalysis.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/utility.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/version.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so.4.0.0
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so.4
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/lib/arm-linux-gnueabihf/libgromacs.so
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/lib/arm-linux-gnueabihf/pkgconfig/libgromacs.pc
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/cmake/gromacs/libgromacs.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/cmake/gromacs/libgromacs-release.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/cmake/gromacs/gromacs-config.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/share/cmake/gromacs/gromacs-config-version.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/mdlib/simulationsignal.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/cmdlinehelpwriter.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/cmdlineinit.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/cmdlinemodule.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/cmdlineoptionsmodule.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/cmdlineparser.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/cmdlineprogramcontext.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/filenm.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/pargs.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/commandline/viewit.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/fft/fft.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/gpu_utils/hostallocator.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/linearalgebra/eigensolver.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/linearalgebra/matrix.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/linearalgebra/sparsematrix.h
-- Installing: /<<PKGBUILDDIR>>/debian/gromacs/usr/include/gromacs/math/3dtransforms.h
-- Installing: /<<PKGBUILDDIR>>